Packaging more than one IPA into the same output directory will delete all previously created IPA and DSYM files. See also XCodeBuilder.java
...
listener.getLogger().println(Messages.XCodeBuilder_cleaningIPA());
for (FilePath path : ipaOutputPath.list("*.ipa")) {
path.delete();
}
listener.getLogger().println(Messages.XCodeBuilder_cleaningDSYM());
for (FilePath path : ipaOutputPath.list("*-dSYM.zip")) {
path.delete();
}
...
It would be better to just delete files with the correct target name eg. "baseName + ".ipa";" etc.