Experienced a bug when having a track pitched down in track settings. Pitch remains consistent when playing and overdubbing in regular mode. However, tried to go into the looper and the track pitch reverted back to the original sample pitch while in record mode.
I think this bug is similar to at least one that was fixed before regarding pitch change not holding when recording overdubs on a multi slice mode if I remember correctly.
It sounds like you used Playback Override to change the pitch during playback. That does not change the pattern.
To change the pitch recorded in the pattern, use Record Overwrite. Or, go to the pitch settings for that track (Shift+A in Pitch mode) and select Modify Pattern.