Can you send us your Skyline document?
I am not sure whether we would be able to implement this feature, but it would be good to be able to take a look at a real world scenario where it would be useful.
Why do you want to get rid of these transitions? How are they causing problems? SRM method taking too long?
You can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.
If that .zip file is less than 50MB you can attach it to this support request. Otherwise, you can upload it here:
One tricky thing about trying to implement "remove duplicates" with a sort of "fuzzy matching" is that this fuzzy matching is not transitive. That is, you might have three transitions: 400.01, 400.03, and 400.05 and you tell Skyline that duplicate transitions are within 0.03 of each other. In the end, Skyline might leave you with just the transition 400.03, or it might remove that one transition and leave you with 400.01 and 400.05.