Same problem. Were you able to find a solution?
JohnnieWa1ker
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I also faced such a problem for the SwiftMessages library, which is simply present in the local SPM framework.
Appeared only on XCode 13 beta 3, before that on XCode 12 everything works fine.
5 years have passed, but the problem is still relevant (Xcode 12.4).
As a temporary solution, Xcode has to be closed completely. After that, the project is re-indexed and there is enough memory to rename 2-3 classes, after which the action has to be repeated.