I’m surprised no one has commented as I would assume there would be quite a few folk who use both.
I don’t use either NINA or GSS but have used EQMOD for 6 years. EQMOD is primarily star alignment or sync point alignment which creates a pointing model for accurate Goto.If your opting to plate solve best just use plate solving software and not get EQMOD involved. Regarding NINA and GSS with tracking issues after a flip I’d check all the obvious things first like -
Updating drivers
Check your versions for known bugs
GSS settings relating to meridian flips
NINA settings relating to meridian flips
Ensure your using Ascom pulse guiding with PHD2 ( not ST4 )
Ensure you have saved your PHD2 calibration in Brain (Auto restore)
And a host of other checks ……
Maybe join the GSS Google Groups and the NINA discord for additional help
https://discord.com/invite/fwpmHU4
https://gss.groups.io/g/main/topics
Hope you sort your issue sooner than later
Cheers
Martin