If you changed the name of the feature class, and then attempted to check in the data but it not worked. This would mean the .axf file initially created from the original feature class, needs to be the same upon check out. Now you went back and changed the name of the feature class back to the original name, then attempted to re-check in the data then it may think the data has already been checked in. I would suggest the following work flow to save the data which has been collected, within ArcPad Studio.
arcpadstudio
1. Open arcpadstudio
2. Navigate to axf file
3. Open axf file
4. Right click on feature layer
5. Export to shapefile
ArcMap
1. Open mxd file with feature class
2. Add shapefile that was created out of arcpadstudio
3. Make only shapefile selectable
4. Begin a Edit session
5. Open attribute table for shapefile
6. Select all records
7. Edit pull down
8. Copy
9. Edit pull down
10. Paste
11. You should be prompted to paste records into Feature class (Ok)
12. Editor
13. Stop and Save Edits