Just as a note, it’s ok to delete in the content browser when the red button says ‘delete’, obviously when it says ‘force delete’, then you’re probably asking for trouble. 
I know you’re just saying this as a tip, but could that be part of this issue or is it just because of some other issue?
Everything in the content browser ( the content folder of your project ), is linked. You can see it by right clicking on something and choosing ‘reference viewer’.
If you routinely use the force delete button or delete things from outside the editor ( using windows ), those references will break. And that will lead to unpredictable behaiviour.
Have you been doing any of this sort of thing?
If you haven’t and you’re just using the plain ‘delete’ button, then even if you have a slow PC, it would just take a long time to do the job.
How old is your project?
Hello,
Earlier today I made this post which details the safety of deleting asset pack files within a project.
I finally got around to doing that, however with a few things (maps, skybox textures, etc) unreal crashes.
What seems to be the problem here?
UPD:
The issue stems from deleting Maps and HDR files.