We currently have two methods of fixing up redirectors: the ResavePackages commandlet and the Fix Up option within the editor. While the editor's option correctly handles collections via FAssetFixUpRedirectors::SaveReferencingCollections, there's no equivalent functionality in UResavePackagesCommandlet. As a result, fixed-up assets will be missing from collections, and opening the collection asset in a text editor will show that the old path is still there.
UE4Editor.exe <Project Location> -run=ResavePackages -fixupredirects -skipfails -autocheckoutpackages -ignorechangelist -projectonly -crashforuat -stdout
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-57027 in the post.