Change files outside of eclipse then deliver with eclipse

Imagine a scenario where you have a migration that takes an initial baseline of files from another change control tool into RTC, we then want to drop the current files in the old change control tool over the top of that baseline, and at the same time make them register in the pending changes view and be a available for delivery. I can obviously deliver them to two components very easily but I want to generate the history and changesets in RTC

I was hoping that I would be able to import the new set of files over the top of the old set of files and have them appear in the pending changes view simply, but neither that or merging the files into the workspace with a compare tool seems to work. The import option seems most promising but gives conflict errors that I cannot ignore, the synch over the workspace option may work with existing files, but not for any new/ removed files (they do not appear in the package explorer and the refresh sandbox / package explorer options do not help). This operation would be simple in the old tool, getting a bit frustrated ;-) Any pointers?

Cheers

Richard