Ok, thanks for the advice. So, in your experience, what would be the best way to go about animating to avoid this issue? I assume that if you need to be creating new documents or avoiding certain colors it's not a very smart workflow.
For instance, what if I need to move an entire animation a couple of pixels to the right? I feel like there should be a way to at least group all keyframes to be a ble to manipulate them as a single object.
If we talk about edits other than colour swaps, there are dfferent methods.
One is Edit Multiple Frames.
The other as mentioned before is keeping your stuff nested inside Graphic Symbols, so that you can go on the outside and treat it as one.
It is always a bad idea to work on the main Timeline.
More information how to organise flies for animation:
http://flash-powertools.com/workflow/
http://flash-powertools.com/character-rigging-for-flash-animation/
http://flash-powertools.com/edapt-movie-template-free-download/