Hyper-Retiming, How to disable it in the .qsf?

Retiming normally does not take very long because it is using the post-fit netlist and doesn't make changes to that netlist. All it does is make decisions about moving registers from LABs to hyper-register locations.

Retiming in a different tool would be based on the synthesis netlist. That's a different type of retiming from the hyper-retiming performed on the post-fit netlist by Quartus.

Are you saying that just the hyper-retiming stage itself took 38 minutes or the overall compile was that long?

If just the hyper-retimer is taking that long, then maybe there is some other related setting enabled, or maybe a fast forward compile is being run automatically or something.