Classes seem to disappear from index sometimes

I can't seem to reproduce this in any artificial way, but sometimes opening a file (i.e. when using code navigation) causes all classes in it to be removed from the index (I actually verified it in the index, they were gone, but the file itself was not). As a result, closing the file and then modifying a file you were previously working in that was using a class from that file suddenly causes linting to start complaining that the class no longer exists, whilst I did nothing to actually modify the file myself.