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Hello,
For the first issue, how the tools on GPS Analyst and within the ArcPad Data Manager toolbar work is that when checking an AXF file back into ArcMap, the path to the original data that the AXF was created from, must be exactly the same or the tool will not be able to find where to check the data back into. Unfortunately there is no way to change the path that the AXF file is referencing. In order to be able to tell what that path is, open 'Get Data From ArcPad' and path out to that AXF file. At the top will be the path listed. I know that you need to use GPS Analyst to actually check the data in, this is just a way to see the path its referencing.
For the second issue, unfortunately, once an AXF file gets successfully checked back into ArcMap, there is no way to re-checking those same features from that same copy of the AXF. The workflow that you are currently working, retrieving a copy from the mobile device, is the only way to check in those features again. I understand that the mobile device does get 'cleaned out', so I would recommend making a backup copy of that ArcPad project folder from the mobile device onto a network or local drive somewhere, so that a copy could be retrieved if needed. For the issue with ArcMap crashing upon checkin, if that is a reoccurring issue I would recommend performing an uninstall/reinstall of GPS Analyst or, using test data, try to see if ArcMap crashes if the data is checked back in using the ArcPad Data Manager toolbar.
I hope this information helps.
Thank you.