When I attempt to add an MXD to Pro from a folder that contains several 10.3.1 MXDs, Pro doesnt show any MXDs in that folder. If i choose some other folders with MXDs, it recognizes some. Are there some reasons that Pro doesn't recognize/import MXDs?
Maybe there is data in your mxd that Pro cannot recognize, so it does not import the mxd at all (e.g. personal geodatabases are not available to Pro as personal geodatabases can only be utilized in a 32 bit environment).
The do have GDBs and SHPs. But no MDBs.
Can you try copying the problematic mxds to a folder where you can import mxds from to see if that makes a difference?