One way round it is to ensure the offending sync operation occurs in a region where EQMOD will reject it. So long as you are using releatively recent versions of EQMOD the following should be possible:
Set your SGP flip point well past the meridian itself (the more minutes the better). EQMOD will reject sync operations that take place past the meridian so when SGP performs the sync prior to the flip EQMOD raises an execption that SGP will catch, ignore, and continue with the flip movement.
Chris.