did you solved the problem ?
i have the same behaviour, i'm using time stamp for the picture naming and after sometime (never the same)
the counter stuck to a value, so as filename are timestamp i see many files with the same number (but with different timestamp), so Ekos continue to acquire images
but image counter does not increase anymore. And after sometime ekos crash (kstar and ekos automaticaly close) and i'm back to the desktop.
typically i have between 2 and may be 20 images max with the same number.