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Possibly I ran into the same problem: using "Compress Build Log Plugin" everything is fine until I choose to rescan the Builds with BFA.
So I think one solution is to "not change the old build log" in this use case using a NullOutputStream instead of a FileOutputStream with the old build log.
In com.sonyericsson.jenkins.plugins.bfa.sod.ScanOnDemandTask.scanBuild(AbstractBuild)
change line
fos = new FileOutputStream(abstractBuild.getLogFile(), true);
to
fos = new NullOutputStream();
Another solution is to check if file is gzipped and then use NullOutputStream or decompress first, change logfile, compress after BFA is done.