It's not just the 'paperwork' - read the DHAN for an 'example' of other issues - a modification to the elevator.
Would you want to fly an aircraft that had a modification to a primary flight control that hadn't been through a design review process in association with the manufacturer/type certificate holder? and was undocumented? Are all of the mods the same? you'd have no way of knowing.
And it's acknowledged that a number of airframes that weren't in service prior to the pause were unserviceable because the 'maintenance contractor' (term used loosely) didn't have the skills to repair them.
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