The jar format is just a rebranded zip format, so it inherits the limitations of that format.
The original zip format has a limit of 65535 entries, so in total in Java 6 and earlier, you can have at most that many classes or other files, combined. Many tools also include directories as entires, and this reduces the entires available for classes and other files.
In java 7, zip64 is supported, with a much higher limit.
I suspect the failure mode, however, won't be randomly missing files, but failure at jar generation time.
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