From looking at the Java error log, I suspect it's a bug and/or memory leak in Java's handling of zip files. I'm still trying to confirm that, but given the sporadic nature of the issue that may take some time.
In the meantime, you can work around the problem by using MAT files instead of SBPROJ files. Just change sbiosaveproject and sbiosaveproject to load and save, respectively.
Good luck! -Arthur
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