In addition to setting the relevant column to false() as suggested by @LN for variables that have been dropped from the data collection, I am copying pasting here the solution kindly provided by @aurdipas to handle groups of variables that have been in another group in the same form - in case anybody else ends up with the same issue.
- Use the ODK XLSForm Offline (release v2.0)
- you can uncheck the option to validate. So the form with the X variable with same name in different groups will be converted.
- only thing that you would need to change is the way reference to this variables if you use these in calculation/relevant/constraint columns
- you can not use the typical
${a3_b_2}but you would need to use the full path/data/previous_enrolment/a3_b_2(as an example) - after you convert it it uploads on Central smoothly
On a note, you need to manually edit your XML form if you moved child groups within parent groups (as the converter does not allow for several groups with the same names).
Still not ideal for everyday data management, but handy in "emergency" situations.
You then have to merge "duplicated" columns from the export (but this was expected as the structure had been changed) so that the change is transparent for the team analysing the data.