I've done it and it is a slight issue. A lot of it depends on how the ball is wrapped and how much you are doing like that.
If the outer layer is wrapped on top it's not so bad. If it's wrapped around the ends it's a pain.
I always do it that way for a double strand chain when crocheting.
For a whole skein I find it easier to strip it out and rewrap a center pull ball with the two strands together.
It's the same issues while stripping and wrapping but it's not going on while you're trying to work.