big design uses few resources

The debugger runs through jtag and is an output, so the logic that drives it should not be synthesized out. Quartus removes logic when it doesn't drive anything at all. The other thing that happens is things can get synthesized out due to something not hooked up right or something like that.

One trick is to use Design Partitions if you have a license for them. Put on a hierarchy, they keep all the inputs and outputs and therefore the internal logic. (You actually have to have one output of the partition drive logic or a top-level output, otherwise it will get removed). But that is probably not going to to work, as Quartus is removing the logic for a reason, i.e. it doesn't affect the output of your debugger. Keeping the logic through partitions probably won't fix the problem.