I guess it depends on the context.
Yes, it was derived from the "flip side" of vinyl records, however it became a phrase equivalent to: "see you later/soon".
But again, to me it depends on the context.
For example, if someone is about to do something life threatening (or over exaggerated as life threatening) it could mean "see you in the after life", making the flip side, in this case, heaven.
Oh my, I'm gonna jump out of a plane now… Catch you on the flip side.
Another instance where it could be used is obviously just "see you tomorrow". I once heard a theory that the flip side meant something or other about the Earth rotating through its 24 hour cycle, hence making the the flip side the following day.
Finally, the way I always thought it was taken is when you are saying goodbye to someone who you are unsure whether you may see again.
Such as… Well tomorrow is my last day of high school so quite relevantly saying goodbye to classmates and teachers you may never run into again. Or perhaps someone you befriended one day on city transit and probably won't run into again. Or maybe a coworker leaving… Whatever it may be, I thought the flip side was just symbolic for the unknown. To sum it all up, I guess to me it meant "It's uncertain we'll meet again, but I hope we do."