First, I would make a safe copy of all your axf files before you begin altering any of them in this manner just to be safe.
If you have ArcPad Studio, open up any of your axf files in ArcPad Studio. Right-click on a layer definition, and click Show Data. You will now have a SQL command interface and a pane that shows your data. You are now going to run an UPDATE query against your data that alters the value in the AXF_STATUS field. Currently, it should have a value of 16777217 for all records that were checked-in. If you want the edits in the axf file to modify existing features in your geodatabase, change the value to 2 in the AXF_STATUS field. If the data in your axf file are new data (i.e. new features), change the value of 1 in the AXF_STATUS field.
Type a SQL query with this syntax in the space provided:
UPDATE table_name SET AXF_STATUS=value; (Don't forget the semi-colon. It is required.)
where table_name is the name of the feature class in caps (e.g. REACHES) and value is either 1 or 2 depending on whether you are creating new data or updating existing data in your geodatabase.
Now hit the red exclamation point in your toolbar which is the Execute tool and it will execute the SQL command. You should then get a message that X number of records were updated. If you get an error, you have likely used the wrong syntax.
To view the changes, close the axf file and reopen in ArcStudio, and do Show Data again or you may just be able to run this SQL query:
SELECT * FROM table_name;
Be aware that if you have edited any of these features in your geodatabase that you are checking-in via the axf, your edits will be lost.
Now, check-in your axf file as usual. Repeat the process for each axf file.
This has worked for me, but I was not using data that had integrated GPS data, so it may not work for you. This is entirely at your own risk to use the solution I have suggested.
