I just upgraded system from Jenkins 1.644 to 2.40
At the same time I have upgraded PTC integrity Plugin from 1.3.6 to 2.0.2
I have updated config of some build job (at timeout condition) and started to test.
Unfortunately, synchronizing workspace failed buy timeout did not happened after specified time!

Below part of the corresponding log:

Time Elapsed 00:00:02.45
Success build fororg.jenkinsci.plugins.conditionalbuildstep.singlestep.SingleConditionalBuilder@f00640
Change Log: http://ds-jenk2-1.biotronik.com:8080/job/TDE.Common_Libraries-ECM_Utilities/343/changes
Build Log: http://ds-jenk2-1.biotronik.com:8080/job/TDE.Common_Libraries-ECM_Utilities/343/console
Preparing to execute si projectinfo for /repository/TDE/Common_Libraries/ECM_Storage/project.pj
Preparing to execute si viewproject for #/repository/TDE#Common_Libraries/ECM_Storage
Checkout directory is D:\Jenkins_ROOT\TDE\Common_Libraries\ECM_Storage
A clean copy is requested; deleting contents of D:\Jenkins_ROOT\TDE\Common_Libraries\ECM_Storage
Populating clean workspace...
A Timeout Exception was caught. Failed to checkout contents of file!
null
ERROR: Failed to synchronize workspace!
Retrying after 10 seconds
Change Log: http://ds-jenk2-1.biotronik.com:8080/job/TDE.Common_Libraries-ECM_Utilities/343/changes
Build Log: http://ds-jenk2-1.biotronik.com:8080/job/TDE.Common_Libraries-ECM_Utilities/343/console
Preparing to execute si projectinfo for /repository/TDE/Common_Libraries/ECM_Storage/project.pj
Preparing to execute si viewproject for #/repository/TDE#Common_Libraries/ECM_Storage
Checkout directory is D:\Jenkins_ROOT\TDE\Common_Libraries\ECM_Storage
A clean copy is requested; deleting contents of D:\Jenkins_ROOT\TDE\Common_Libraries\ECM_Storage
Populating clean workspace...
A Timeout Exception was caught. Failed to checkout contents of file!
null
ERROR: Failed to synchronize workspace!
Retrying after 10 seconds
Change Log: http://ds-jenk2-1.biotronik.com:8080/job/TDE.Common_Libraries-ECM_Utilities/343/changes
Build Log: http://ds-jenk2-1.biotronik.com:8080/job/TDE.Common_Libraries-ECM_Utilities/343/console
Preparing to execute si projectinfo for /repository/TDE/Common_Libraries/ECM_Storage/project.pj
Preparing to execute si viewproject for #/repository/TDE#Common_Libraries/ECM_Storage
A SQL Exception was caught!
Table/View 'SCM_C380AD5E_FCBF_4350_8B88_0FE304E3C602' does not exist.
ERROR: Caught Derby SQLException!
Retrying after 10 seconds
Build was aborted
Aborted by Grigoriy Milman
Archiving artifacts
Recording fingerprints
Build failed! Skipping Integrity Checkpoint step!
Started calculate disk usage of build
Finished Calculation of disk usage of build in 0 seconds
Started calculate disk usage of workspace
Finished Calculation of disk usage of workspace in 0 seconds
Warning: you have no plugins providing access control for builds, so falling back to legacy behavior of permitting any downstream builds to be triggered
Finished: ABORTED