Had exactly the same problem deleting some maps.
In Windows10 I went to the root folder of my project, wrote cmd in the top textbox so It opened a command prompt at my root projects folder. Used “XXXXX.uproject -NoLoadStartupPackages” to open my project with that flag.
Then you can remove those files with no warnings or any other problems.
At least this worked for me.
I know its so late but until today I havent seen this warning ahead.