When we exported an AXF, the editable layer had all its fields turned on. When we bring it back in, months later, even if a field wasn't set up for editing outside the office, the values in the field at the time of export overwrite the values in the SDE feature class it's imported into, which have been edited in the meantime in the office. Is it possible to delete fields in an old AXF, like one would delete fields in a shapefile or feature class, thereby preventing a specified group of fields from being overwritten by the older values in AXF when it's brought back in to the SDE feature class?
Have you tried just exported the AXF into a shapefile in ArcPad Studio? This is usually the last resort but worth a try as you can then remove the fields you dont want from the shapefile.
There is also an .axf to geodatabase tool in FME and Data Interop that could also help if you didn't want to use shapefiles.
You can also use ArcPad Studio to perform SQL queries on your .axf data to update values if required.
If this workflow happens often, I would recommend you use versioning in your GeoDatabase. That way, when multiple edits to the same record occur (be it from ArcPad or from elsewhere), you can manually reconcile any conflicts detected. For the ArcPad workflow, you could enforce that your field users check out / check in to a version that's dedicated for mobile data capture.