If you edit the mesh yourself when you are using the Multires modifier, you will get an error.
Use a brush to organize the protruding parts
I don’t know if there’s any other way.
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Welcome …
…IDK if i understood this correctly but: Do not use booleans on a multires !!
You are supposed to have finished your base mesh and use a multires modifier to add details. You may try Apply Base to re-change the base… even Reshape by using a modified copy.