StubIndex Version does not properly index on update

So I am having a problem, and I am not sure what could possibly cause it, or possible solutions. I have a number of indices, and every time I update the stub version, the IDE appears to be re-indexing the files on start, but the indices are not fully formed at all. One or two items are sometimes indexed, but most things are not. My inspections and annotations that require indices flag a number of errors, that it would not, had the indexes been formed. 

To fix this problem, I have to quit the application normally, and restart it. If I invalidate and clear caches, the problem returns until the IDE is quit normally, and started normally. At this time, the indexing process is re-run, and then all annotations and inspections work as they should. I am worried that if this problem exists when I push the next update, users will try to invalidate caches as I did, and find that the problem has not been fixed. I do not know how to tell them to quit and then start the application as normal.

Is there a way to force indices to rebuild after they have been incorrectly or partially built? My plugin is quite involved, so I do not know where to look, or what code to show you for tips. Any insights would be appreciated.

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Did you get "Version has changed for stub index .." in idea.log? Could you please provide full idea.log after (fake) update of stub version? Are sources of your plugin available?

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