I've had the same issue when getting out of timewarp. It sinks my periapsis by about 45km and sometimes more. It's combined with the issue that when close to the Mun (only body I went exploring so far) the periapsis decays slowly, which force me to timewarp to hold the orbit stable.
So it's a vicious circle, periapsis decays while apoapsis goes up, you timewarp and when getting out it you've made the situation worse
@Devs, I've got video recording of the issue if you want:
https://we.tl/t-mwXxLrvgF7
