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yes. Take them off, they don't help with door dings anyways. Get a hair dryer and some goof off or other residue remover. If you want to do a good job take your time pulling them off. They are just held on by two sided tape. Getting the residue off is the hardest part, but it will come off with lots of rubbing.
I would suggest having a body shop weld in metal and then repaint, thats the best way to do it, its a little thick for bondo, it will last for a while but will probally crack. But if you do use bondo, you have to sand where its gonna go otherwise it won't adhere.