We have multibranch pipeline projects with webhooks activated. We noticed that if there is an open PR for a branch, both the branch and PR pipelines are disabled when we make a commit. This behavior is very annoying as we have to click the "Scan Multibranch Pipeline" all the time to enable the pipelines.

Pipeline Logs are not providing any clear indication of what's happening but reproducing is as easy as creating a new branch, and a PR for that branch. Then, make a simple commit and the pipelines are disabled.

I have attached  the config.xml of the multibranch pipeline to give you the details of the configuration of our pipelines.

Please help us as it is annoying our Jenkins users.

Thanks in advance.

 
Jenkins: Version 2.504.3
OS:  Linux 5.14.0-570.24.1.el9_6.x86_64
Java: 17.0.15 OpenJDK 64-Bit Server VM
Plugin Version: 4.2.0 and 5.0.0

Jenkins Plugins Versions
mjenkins003: OWASP Markup Formatter Plugin (antisamy-markup-formatter): 173.v680e3a_b_69ff3
mjenkins003: Apache HttpComponents Client 4.x API Plugin (apache-httpcomponents-client-4-api): 4.5.14-269.vfa_2321039a_83
mjenkins003: Apache HttpComponents Client 5.x API Plugin (apache-httpcomponents-client-5-api): 5.5-166.v870a_96374f91
mjenkins003: ASM API Plugin (asm-api): 9.8-163.vb_2a_96d3f9c3c
mjenkins003: Bitbucket Server Integration (atlassian-bitbucket-server-integration): 4.2.0
mjenkins003: Basic Branch Build Strategies Plugin (basic-branch-build-strategies): 275.vde2351b_4a_58b_
mjenkins003: Bitbucket Pipeline for Blue Ocean (blueocean-bitbucket-pipeline): 1.27.21
mjenkins003: Common API for Blue Ocean (blueocean-commons): 1.27.21
mjenkins003: Config API for Blue Ocean (blueocean-config): 1.27.21
mjenkins003: Blue Ocean Core JS (blueocean-core-js): 1.27.21
mjenkins003: Dashboard for Blue Ocean (blueocean-dashboard): 1.27.21
mjenkins003: Display URL for Blue Ocean (blueocean-display-url): 2.4.4
mjenkins003: Events API for Blue Ocean (blueocean-events): 1.27.21
mjenkins003: Git Pipeline for Blue Ocean (blueocean-git-pipeline): 1.27.21
mjenkins003: GitHub Pipeline for Blue Ocean (blueocean-github-pipeline): 1.27.21
mjenkins003: i18n for Blue Ocean (blueocean-i18n): 1.27.21
mjenkins003: JWT for Blue Ocean (blueocean-jwt): 1.27.21
mjenkins003: Personalization for Blue Ocean (blueocean-personalization): 1.27.21
mjenkins003: Pipeline implementation for Blue Ocean (blueocean-pipeline-api-impl): 1.27.21
mjenkins003: Blue Ocean Pipeline Editor (blueocean-pipeline-editor): 1.27.21
mjenkins003: Pipeline SCM API for Blue Ocean (blueocean-pipeline-scm-api): 1.27.21
mjenkins003: REST Implementation for Blue Ocean (blueocean-rest-impl): 1.27.21
mjenkins003: REST API for Blue Ocean (blueocean-rest): 1.27.21
mjenkins003: Web for Blue Ocean (blueocean-web): 1.27.21
mjenkins003: Blue Ocean (blueocean): 1.27.21
mjenkins003: Bootstrap 5 API Plugin (bootstrap5-api): 5.3.8-876.vb_c62a_27d9a_77
mjenkins003: bouncycastle API Plugin (bouncycastle-api): 2.30.1.81-264.v95c79c0e772c
mjenkins003: Branch API Plugin (branch-api): 2.1244.vf95c81f1641c
mjenkins003: Build Discarder Plugin (build-discarder): 158.vce570d01ce4c
mjenkins003: Build Timeout (build-timeout): 1.38
mjenkins003: Caffeine API Plugin (caffeine-api): 3.2.2-178.v353b_8428ed56
mjenkins003: Checks API plugin (checks-api): 373.vfe7645102093
mjenkins003: Bitbucket Branch Source Plugin (cloudbees-bitbucket-branch-source): 936.4.3
mjenkins003: Folders Plugin (cloudbees-folder): 6.1040.v8a_e6330a_54e3
mjenkins003: Command Agent Launcher Plugin (command-launcher): 123.v37cfdc92ef67
mjenkins003: commons-lang3 v3.x Jenkins API Plugin (commons-lang3-api): 3.18.0-98.v3a_674c06072d
mjenkins003: commons-text API Plugin (commons-text-api): 1.14.0-194.v804a_dc3a_1b_d8
mjenkins003: Config File Provider Plugin (config-file-provider): 994.v3d4a_5fa_f353a_
mjenkins003: Configuration as Code Plugin (configuration-as-code): 1985.vdda_32d0c4ea_b_
mjenkins003: Coverage Plugin (coverage): 2.2941.v08df75b_767f1
mjenkins003: Credentials Binding Plugin (credentials-binding): 702.vfe613e537e88
mjenkins003: Credentials Plugin (credentials): 1447.v4cb_b_539b_5321
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mjenkins003: Display URL API (display-url-api): 2.217.va_6b_de84cc74b_
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mjenkins003: Docker Pipeline (docker-workflow): 621.va_73f881d9232
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mjenkins003: ECharts API Plugin (echarts-api): 6.0.0-1146.v5c8f3b_8f0573
mjenkins003: EDDSA API Plugin (eddsa-api): 0.3.0.1-19.vc432d923e5ee
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mjenkins003: Environment Injector Plugin (envinject): 2.926.v69c9b_3896a_96
mjenkins003: Favorite (favorite): 2.253.v9b_413168133b_
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mjenkins003: Font Awesome API Plugin (font-awesome-api): 7.0.1-859.v128d3a_efb_6e5
mjenkins003: Forensics API Plugin (forensics-api): 3.1754.v2a_6613b_77002
mjenkins003: Git client plugin (git-client): 6.4.0
mjenkins003: Git plugin (git): 5.7.0
mjenkins003: GitHub API Plugin (github-api): 1.330-492.v3941a_032db_2a_
mjenkins003: GitHub Branch Source Plugin (github-branch-source): 1864.v411feec5e78e
mjenkins003: GitHub plugin (github): 1.45.0
mjenkins003: Gson API Plugin (gson-api): 2.13.2-173.va_a_092315913c
mjenkins003: Handy Uri Templates 2.x API Plugin (handy-uri-templates-2-api): 2.1.8-36.v85e4cb_234a_13
mjenkins003: HTML Publisher plugin (htmlpublisher): 427
mjenkins003: Instance Identity (instance-identity): 203.v15e81a_1b_7a_38
mjenkins003: Ionicons API (ionicons-api): 94.vcc3065403257
mjenkins003: Jackson 2 API Plugin (jackson2-api): 2.20.0-411.v6ef8fdee4fe9
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mjenkins003: Jakarta Mail API (jakarta-mail-api): 2.1.3-3
mjenkins003: Javadoc Plugin (javadoc): 354.vee1a_660b_4990
mjenkins003: JavaBeans Activation Framework (JAF) API (javax-activation-api): 1.2.0-8
mjenkins003: JavaMail API (javax-mail-api): 1.6.2-11
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mjenkins003: Oracle Java SE Development Kit Installer Plugin (jdk-tool): 83.v417146707a_3d
mjenkins003: Design Language (jenkins-design-language): 1.27.21
mjenkins003: Joda Time API Plugin (joda-time-api): 2.14.0-149.v1c3ce991d1b_9
mjenkins003: JQuery3 API Plugin (jquery3-api): 3.7.1-594.vb_3864f326cf0
mjenkins003: JSch dependency plugin (jsch): 0.2.16-95.v3eecb_55fa_b_78
mjenkins003: JSON Api Plugin (json-api): 20250517-173.v596efb_962a_31
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mjenkins003: JUnit Plugin (junit): 1355.v45e2ea_65863c
mjenkins003: Kubernetes Client API Plugin (kubernetes-client-api): 7.3.1-256.v788a_0b_787114
mjenkins003: Kubernetes Credentials Plugin (kubernetes-credentials): 206.vde31a_b_0f71a_c
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mjenkins003: Mailer Plugin (mailer): 522.va_995fa_cfb_8b_d
mjenkins003: Matrix Project Plugin (matrix-project): 858.vb_b_eb_9a_7ea_99e
mjenkins003: Mercurial plugin (mercurial): 1323.ve69d2a_db_8a_b_d
mjenkins003: Metrics Plugin (metrics): 4.2.33-484.v2fcd689980d1
mjenkins003: Mina SSHD API :: Common (mina-sshd-api-common): 2.16.0-167.va_269f38cc024
mjenkins003: Mina SSHD API :: Core (mina-sshd-api-core): 2.16.0-167.va_269f38cc024
mjenkins003: Nexus Platform Plugin (nexus-jenkins-plugin): 3.20.9-01
mjenkins003: Dev Tools Symbols API Plugin (oss-symbols-api): 392.v27a_482d90083
mjenkins003: Pipeline: Build Step (pipeline-build-step): 571.v08a_fffd4b_0ce
mjenkins003: Pipeline Graph Analysis Plugin (pipeline-graph-analysis): 245.v88f03631a_b_21
mjenkins003: Pipeline: Groovy Libraries (pipeline-groovy-lib): 752.vdddedf804e72
mjenkins003: Pipeline: Input Step (pipeline-input-step): 534.v352f0a_e98918
mjenkins003: Pipeline: Milestone Step (pipeline-milestone-step): 138.v78ca_76831a_43
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mjenkins003: Pipeline: Declarative (pipeline-model-definition): 2.2273.v643f36ed9e94
mjenkins003: Pipeline: Declarative Extension Points API (pipeline-model-extensions): 2.2273.v643f36ed9e94
mjenkins003: Pipeline: REST API Plugin (pipeline-rest-api): 2.38
mjenkins003: Pipeline: Stage Step (pipeline-stage-step): 322.vecffa_99f371c
mjenkins003: Pipeline: Stage Tags Metadata (pipeline-stage-tags-metadata): 2.2273.v643f36ed9e94
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mjenkins003: Plain Credentials Plugin (plain-credentials): 199.v9f8e1f741799
mjenkins003: Plugin Utilities API Plugin (plugin-util-api): 6.1167.v022176c7e0ca_
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mjenkins003: Resource Disposer Plugin (resource-disposer): 0.25
mjenkins003: Role-based Authorization Strategy (role-strategy): 799.v5b_e7b_ecc231e
mjenkins003: SAML Plugin (saml): 4.583.vc68232f7018a_
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mjenkins003: SnakeYAML API Plugin (snakeyaml-api): 2.3-125.v4d77857a_b_402
mjenkins003: SonarQube Scanner for Jenkins (sonar): 2.18
mjenkins003: Server Sent Events (SSE) Gateway Plugin (sse-gateway): 1.28
mjenkins003: SSH Credentials Plugin (ssh-credentials): 361.vb_f6760818e8c
mjenkins003: SSH Build Agents plugin (ssh-slaves): 3.1071.v0d059c7b_c555
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mjenkins003: SSH server (sshd): 3.374.v19b_d59ce6610
mjenkins003: Structs Plugin (structs): 353.v261ea_40a_80fb_
mjenkins003: Throttle Concurrent Builds Plug-in (throttle-concurrents): 2.18
mjenkins003: Timestamper (timestamper): 1.30
mjenkins003: Trilead API Plugin (trilead-api): 2.209.v0e69b_c43c245
mjenkins003: Active Choices Plug-in (uno-choice): 2.8.8
mjenkins003: Variant Plugin (variant): 70.va_d9f17f859e0
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mjenkins003: Pipeline: Basic Steps (workflow-basic-steps): 1079.vce64b_a_929c5a_
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mjenkins003: Pipeline: Nodes and Processes (workflow-durable-task-step): 1464.v2d3f5c68f84c
mjenkins003: Pipeline: Job (workflow-job): 1546.v62a_c59c112dd
mjenkins003: Pipeline: Multibranch (workflow-multibranch): 821.vc3b_4ea_780798
mjenkins003: Pipeline: SCM Step (workflow-scm-step): 452.vdf1ca_c8d3a_87
mjenkins003: Pipeline: Step API (workflow-step-api): 706.v518c5dcb_24c0
mjenkins003: Pipeline: Supporting APIs (workflow-support): 989.va_20a_1a_57710a_
mjenkins003: Workspace Cleanup Plugin (ws-cleanup): 0.49