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Please see defect #240371. I've debugged a little with some additional logs on System.err (see attachment). It seems that the library reference propeties were removed through helper.putProperties() and both the resource and project are marked as modified, but for some reason, the disk file still contained old data even long (minutes) after I removed the files from the explorer. After I made an unrelated change later (i.e. turn on deprecation for compiler) that also affects properties, the project.properties received correct content including library removal.
Created attachment 145100 [details] Diagnostics from the testing The log file was captured from 2 actions (see original scenario for issue #240371 in comment 8) 1/ add libraries to the project. After that, the disk file correctly received the added library references 2/ removed libraries from the project. Disk file was not changed. See the part of log file after === mark.
*** This bug has been marked as a duplicate of bug 241414 ***