Well, let me put it this way - the exclusions were never meant to contain huge lists. Having a lot of exclusions suggests something strange/bad is happening on the machine (say there's a lot of false positives - but that should be solved by fixing the false positives on our side, not by excluding everything), plus it can even slow things down (because for every scanned or accessed file, the whole list needs to be checked... again and again).
Yes, there may be some limit, but it's hard to say what it is (some features may not be affected, some might - by features I mean e.g. on-access vs. on-demand scanning). But the limit won't be the number of exclusions, but rather the overall length of all the added text. My guess would be a few kilobytes of text.
So, I wouldn't be surprised if the list got truncated at some point (either "visibly", or the exclusions at the end wouldn't work). However, it definitely shouldn't clear the whole list as you describe. I'm not sure if I understand correctly what's actually happened... so that "cleanup" of the exclusion list happened just one time and since then you added all the exclusions and it works now, or are you saying that whenever you add a specific(?) path enclosed in quotes, the list gets cleared?