The two cover sheets are likely because three different agencies contribute to/access Intellipedia. JWICS is for Top Secret information. SIPRNET Secret and NIPRNET is for Unclassified information.
So, something could be on JWICS’s Intellipedia archive but also be in SIPRNET and NIPRNET’s as well. Some of the information on each of them would have to be excluded at each level of classification.
Example: I live in Florida. I have a dog. The dog is trained for drug detection (not really, it’s an example).
Information that could be on each level:
I live in Florida.
I live in Florida. I have a dog.
I live in Florida. I have a dog. The dog is trained for drug detection.
So, your first FOIA request should have pulled all NIPRNET information on Trump. The second response means either the first request resulted in some information being held back due to his pre- inauguration status and/or a new file at a higher level of classification would necessarily be created for anyone elected to high office once they’re sworn in and/or have access to information formerly above their pay grade.
In the case of POTUS I would expect him/her to have a JWICS file on them at the least in order to know who is accessing them and who should not be allowed to.
Good report, though. #NEVERTRUMP