I make True-Nukes, and I've had a crash reported, which seems to be common to a few mods like this. When destroy is called on huge numbers of entities, it can cause the callbacks to not happen properly (or so it seems).
This means that calling destroy with raise_destroy=true can cause a crash. The fix should be fairly simple, in control.lua, change FilteredChunk:removeFilter, and make the if statement check valid first:
if not f.valid then
table.remove(self.filters, i)
else if f.unit_number == filter.unit_number then
table.remove(self.filters, i)
break
end
Then it should work nicely (I can't test this as I can't make the bug happen reliably...). The original report is here:
https://mods.factorio.com/mod/True-Nukes/discussion/626d8e9b3f4eac6fa2ad7d79