You can create this file with Write File button on INDI Align tab. Try this:
1) As soon as you start your system (you can use simulation option for EQMod) go to INDI Align tab
2) Click Clear List
3) Click Write File
This way you create empty list in AlignData.xml
If you don't clear the list before writing the file (and you have align points on the list, which are added each time you do plate solving and syncing) you can maintain persistent list of align points between sessions. I wouldn't go for it though if your mount is reset each time before session.