Unfortunately paint effects have a mind of their own, so it would be best to render out your stuff and reimport it to be used as a matte or whatever you have in mind. While generally copy&paste should work, there are several logic holes in the effect that often prevent it like mixing stroke durations and that sort of thing. This stuff is simply seriously outdated...
Thank you mate!
It's because the piece you have painted on, has been cropped. The paint stroke's position in sense of timeline is fixed to the footage's timecode (i had this problem when taking a piece of footage that I had cropped in Premiere pro - and then linked it to After Effects. Giving me the full piece of footage, but cropped to suit what Premiere had told it.
Once I had painted on it, even though the strokes started at 0:00 on after effects, it would be 4 minutes in on the original file.
The solution is to extend the layer you have pasted the copied paint strokes onto, keep extending the length of the layer and you will find the paint strokes much further along the timeline.