How to isolate two plasmids from E. Coli strand?
A retransformation should get you a pure plasmid. Transform the plasmid mix into empty E.coli (don't use too much DNA), plate on Kan / Amp depending on what you need. The probability that one cell took up both plasmids is extremely low, and you could check with colony PCR just to be sure.

Otherwise: ask around, there must be (old) stocks of the single plasmids around, or glycerol stocks of E.coli containing only one of the plasmids.  

Third option: take a look at your mutagenesis method. For your needs there might be techniques around that'll work on a mixture of plasmids. If you just need one variant or a single site saturation library you could use Quikchange for example. I don't see a reason why this wouldn't work on a mix of plasmids.