If After Efects, if you use the clone tool correcly (set it to single frame), you'll have no echo and it's super easy to use and do. Much better than in LR.
If you want to preserve the cloning when doing Auto Transition in LRT, press "Ctrl" while clicking on Auto Transition.
Another option is to do the cloning at the very end of the workflow, before exporting.

I used to remove birds frame-by-frame in LR too (now I shoot longer exposures), and once I did accidentally sync all my hard work away, oops. I now know that edits on individual images (like bird removal) should be usually done very last, before rendering :-)

We've all been there... :-) I have started to edit each frame too. Tedious work, but it gives the best result.