I have run into a couple of different mods that have problems with the surface clear method:

https://mods.factorio.com/mod/stack-combinator/discussion/625b72ad92bac00575ec5121
https://mods.factorio.com/mod/SearchlightAssault/discussion/627ccaa7ec89a01112db9795

Would it be possible to have a whitelist of entities that are manually deleted prior to the surface clear?

Interesting idea! I checked out both, and in both cases it's definitely a fault of those mods with one or more potential fixes. It's obvious that the "fix" from the last update would cause performance issues because it stopped filtering events. All that said, I like this idea because it's something that we can control on sometimes faster timelines than other, maybe abandoned mods. I'll look into making a framework for this.

SearchlightAssault has been updated to fix the issue happening there. In this case, it was definitely an oversight on my part.

Even if it were just a delimited list in the mod settings, it might help in avoiding (or at least temporarily minimizing) some of these edge cases.

SearchlightAssault has been updated to fix the issue happening there. In this case, it was definitely an oversight on my part.

Sorry, I wasn't trying to call out your mod in particular; I've run into at least a dozen others that display some degree of undefined behavior in the sandbox, SLA was just the most recent.