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IMO, it's safe to delete it. I do it all the time when I restore. If you want to, check that ALL of your purchased tables are visible/playable in BOTH the Paid and the Free versions. If they are, you can delete the app that has the least purchased content. I believe both apps will merge the purchase & content. However, note that I have only done this (deleted) with the Free app since I have only one table purchased under that app. I don't know for sure if it would work the other way around (delete the Paid app). I believe I've done it before but it was so long ago that I don't remember. If all fails, just do a remote backup of your scores and re-install/restore purchases on the whole shebang.

As far as the scores go, as long as you are logged in to the same Farsight account when you play either the Paid or Free, your high scores and goals should remain intact. As a precaution, you can always do a remote backup before deleting the app. Be sure you're logged in to your Farsight account as this is the only way that a remote backup will work.

I can't speak for Game Center since I don't use it, sorry.