Adam,
When you check out your data to axf format (using the ArcPad Data Manager toolbar) a new field gets added behind the scenes called "AXF_STATUS". This status field holds numerical values which indicate what should be done to the features when checking them back in.
For existing features that get checked out but do not get modified, the value in the status field indicates to ArcPad that nothing should be done to the original features. Nothing will get checked back in and nothing will happen to the existing features in the geodatabase.
If you added a new feature, a status number would indicate that and it would be copied into the geodatabase.
Likewise, if you modified an existing feature's attributes, geometry, deleted it, etc, a status number would indicate what action was performed and the necessary changes would be made back in the geodatabase from which the data came.
Hope that helps.