Using Good 64

it depends what kind of dumps they are. nothing malicious will happen, an o means that it's an overdump and it's taking up more space, but that doesnt mean you cant play it. same with most other things, u can probably play them fine with no errors. unless they are bad roms (bad crc or something - meaning the game is corrupt in some way), there should be no need to redownload an files
conkerman

Frankly, if they work, you can still use them. If they won't work, you'd best get another rom.

You can use Bad-To-Goom-Rom collection to make your bad dumps good. Download + instructions from Smiff's site there go to utilities/for roms.