Bobbsy;
Would there be any way AA could have changed or deleted parts of the DFDR data while downloading it?
Essentially, no. The data creation, transmission, conversion, recording, reading/validation and correction process has its own characteristics and marks which are, in the original file, difficult to near impossible to change. Substitution is not a real possibility again because the data is so closely associated with both the histories of all the recorded flights and the aircraft itself. It would take long experience and deep knowledge of flight data systems to make such changes and even more craft to make them "invisible" to other experienced data people. Like all flight safety processes however, spending years and years learning how to do this work tends to weed out dishonesty and politics by one method or another.
A quick read-through of the CAA document "
Approval, Operational Serviceability and Readout of Flight Data Recorder Systems" may help understand why changing the data with sufficient interventions to make others believe they were reading the original aircraft data would be extremely difficult. If a quick read-through is tough sledding, at least read Appendix B.