New computer. Synching issues

Recently purchased a new computer. all photos were copied from old computer to new computer, along with the catalog files, and placed in the Pictures folder with all of the subfolder hierarchy intact.  The only issue was that in LR synch preferences, the folder indicated was not the correct folder; So I changed it to the correct folder i.e. Pictures/Iphone.  (It's named that way because I sync all my iphone photos into LR mobile, and then from there to the iphone folder in LRC).  It was at that point that I made the error of telling LR to transfer the photos. It happily transferred the photos from the correct subfolders into the top level Iphone directory.  Argh!

My thought is to delete (actually I will just move them to a separate folder until I have confirmed that everything is good) all of the photos which are in the Iphone top level directory (which should not have any photos in it) ; I need to know if when LR synch runs again it will pick up all the photos, I just deleted, and synch them from LR mobile back into the Iphone subdirectory in LRC; or is it just going to synch new photos? There must be a way to tell LR to synch everything in Lightroom mobile, not just "new" photos.

I hope that this is clear.

Thanks for everybody's suggestions.