I did the flares, put them back on the truck with new rubber, and it actually looked pretty good, but I ultimately removed them - well, the desert chaparral removed two of them for me. Better with them off if you ask me, but that depends on your use.
I don't do much wheeling on tight trails and like the look and function of the flares. My thinking for lining my flares is that the gaskets are shot and mostly missing on mine and since the liner is thick it would hide these gaps vs. dropping $$ for new factory ones. If they happen to get removed by nature down the road I'll deal with it then.