Are you importing a downloded gedcom DIRECTLY into your main PAF database? Normally we never do this. We import the downloaded file into a (newly-created) empty database with a new name, so that we can look for unwanted duplicates and family lines that are irrelevent to us. Then we carefully select the people we want, write notes about where they connect to our family, and export ONLY THOSE families to a new gedcom, which we then import into our main PAF database after doing a backup. It is a bit more work up-front but it can save you 100 times that amount of time later.
If I were you, I would restore the backup you made immediately before importing the downloaded gedcom, then follow the procedure above.
Or if you don't have a pre-import backup, you might want to make a new backup (i.e. with a new name) then delete all of the newly-imported people. (This only works if you have not merged ANY of the newly imported people.) To do this, go to the File menu, select Export > Partial > Select and select one of the duplicate people you have imported, and set the relationship filter to ALL RELATED > click Select and verify which people are marked with the ">>" symbol as "selected". If you have selected the group of duplicates, click on Delete, otherwise click on Clear and redo the selecting of the group you wish to delete.
You can merge them in PAF. If you merge the individuals, it will also merge their marriages. (See suggestions to someone else in the list archives regarding showing the RINs.)
Merging is one of the things I like least of all (Oh, you already guessed?). It is tedious and tricky and oh, so slow. It is essential that it be done carefully, or you can easily make someone his own father and generally mess-up your database.
If you have started merging the newly-imported people and have no pre-import backup, maybe spend the $20 to buy PAFInsight (www.ohanasoftware.com). It will still be slow but maybe less so, and there is less liklihood of making serious mistakes. It will also allow you to compare and synchronize two PAF databases, and do a few other neat things.
There is no such thing as having "too many backups". They take a few seconds to create and can save you hundreds or even thousands of hours of work. They are an excellent investment.