Most of the discussion on here about possible problems and theoretical
possible problems is just a lot of arm waving.

Your engine is designed to fly with either mag. The reason you take off with
both mags is in unlikely event that one happened to fail you would still be
flying instead of looking for a soft place to crash. The engine will run
fine with either mag or both.

You say your engine was running a bit rough with one mag. I don't know how
new your mags are, but mags do wear. Most likely this only indicates that
the single mag that you were using is not working at peak performance. It's
older, a little worn, but not something you would notice when using both.
Since everything is in pairs, it could also be that the wires or plugs for
that mag are not quite as good; one worn plug or a wire with a cut would
give you the same rough operation. You might want to have your mags, wires,
and plugs looked at but it is not likely that your engine suffered any
damage.