Not really.
You can search-and-replace for the tags with the names ***_0, ***_1 etc. It is a chore though.
I just delete the duplicate tags, and when compiling the error log will link me directly to the locations of the deleted tags. Not much faster though.
The best is to avoid getting the duplicate tags in the first place.
When you copy-and-paste objects between projects, be sure that you dont change for example the connection name in the different projects. If the connection name is different flex will assume that the tags are different and then create the duplicate tags.
Oh, and you can experiment with the "flat copy". It may help in avoiding getting the duplicate tags.