Hi Rvyhmeister,
For something like this it should still be counting the user as completed, but if it's not firing the data stream (as in once the 3rd module is removed, it is not checking and sending the stream), I would honestly recommend double checking with Canvas support regarding this, as they can look more in-depth at the issue, and provide more in-depth information specific to you and your situation.
In theory, the complete/not complete state should be based solely on module requirements, though I'm not sure if checks are in place to retroactively trigger things like certificates if the modules are updated to no longer be required, and the student completed enough to now be active.