If you symlinked your folders then it is a different story. I have used IS both ways. One with virtualization and the other using symlinked folders.
There is no difference in performance. But I keep it that way just in case IS breaks. Then I use keyclone with symlinked folders. I can box without any addons. IS is nice luxury for boxers and I use it almost exclusively.
Since you have multiple wow installs you may look into symlinking your folders for better performance if you continue to use keyclone. If you want to use IS without any sort of backup then having one wow install is enough as IS uses virtual config files and manages multiple wow clients very well.
Clarification needed - Are we talking about multiple installs or linked folders? There is a BIG difference between the two.
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