Deleting harmful files in Defender may have crashed sites

In each of my sites, Defender has listed several potentially harmful files in WordPress core. There were two types of warnings:
Unknown file in WordPress core
This directory doesn't belong to WordPress core

I went through and deleted them all, one by one—and then three of my sites crashed!

I restored the sites but those same warnings in Defender are back.

Here is one site:

Any suggestions?

Thanks in advance,