I don't seem to be able to change the tuning like I could in older versions of Guitar Pro. When I change the tuning from E to Eb in The Instrument Panel, the track immediately bounces back.
It happens both for an old .gp4 file converted to .gpx and with a new .gpx file I created.

This way I can play along to a track without retuning the guitar between E-Eb. Will mark this as the answer.
– Adam.at.Epsilon Jan 18 '18 at 23:51