In short, yes. Without a descriptoin of how you're doing this, I can only speak generally.
The AI timing can be software or hardware timed depending on how you set it up. The DIO will be software timed unless you have strobe/handshaking signals.
If you are software timing your acquisitions (single reads in a loop), just have the operations in different loops, or skip iterations in a single loop for the slower acquisition.
If you are hardware timing your AI, then the DIO can be software timed or strobed, either of which gives you control over the transfer rate.