Mod Organizer 2 and Wyre Bash Help

[Kruppe]

Hello everyone!

This is my first post in these forums, so apologies if it is in the wrong forum.

I want to make a Bashed Patch, and I know how, but I am hesitant to use it, as the first time I made a Bashed Patch Better Cities suddenly started missing a bunch of textures.

Following Kartoffel's tutorial here (https://www.youtube.com/watch?v=gxCdS5fV7dU) I know how to make a Bashed Patch; my question is, if I enable the Bashed Patch, and a bunch of meshes go missing following its activation, is there a way to restore the mods to the way they were before building the Bashed Patch?
Thank you all very much!