Yes, it'll be fine. I would use lacquer thinner or brake cleaner to make sure it's clean tho. Wiping it off with a rag or using solvent will leave an oil residue behind that will not allow as good a seal. In the absence of thinner or brake cleaner you could wipe it down with clean solvent then rub it down with hot soapy (Dawn works well) cloth to remove the oil. It may sound like overkill, but I've seen tons of leaking flanges that simply weren't cleaned well. Also, make sure your bead of sealer is between the bolt holes and the inner edge of the joint, not the outer or it will leak through the bolt holes. It may seem obvious, but I had to split a big AGCO Allis tractor between the trans and diff recently because the previous mech went around the holes just like that. Huge job for a little mistake.
Steve g