8han

I have had this issue too. The workaround is to go above 3x time warp the moment the game allows you (once you leave kerbin atmosphere) and then warp at 4x until you are about to re-enter the atmosphere for another pass. When above 3x time warp the ap and pe stop increasing. This minimises the increase. I had an eve orbiter that almost didn't make it home due to this issue before I figured out the workaround.