I got it to work correctly, I disconnected from source control from inside the engine and run the FixUp commandlet from the command line. This seems to have done the job correctly for me removing all redirectors I know of.
I manually committed after that.
I realize today that my post is quite confusing and I am mixing up many issues together. I will attempt to clear things up here.
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The FixUpRedirectors command in editor does not seem to work correctly for me. It doesn’t remove everything I need it to.
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When using the FixUpRedirectors command in editor with source control, it the editor does not seem to recognize the fact that it needs to commit deletions.
Anyway I will do everything from outside the editor from now on.