You're asking a complicated question, which is impossible to answer.
In general, most of the funding for residency programs comes from CMS. HRSA funding includes a separate program for stand alone children's hospitals with residency programs, and ThCGME which sponsors outpatient programs that are not directly affiliated with a hospital. If your funding comes from one of these, or other, sources, then your CMS GME funding remains fully intact. However, if while in one of these programs you rotate at a hospital and they decide to submit you for reimbursement via CMS -- then your funding can be used. Usually, the residency program and hospital will have an agreement about whether this will happen or not.
There is no way to figure out how much of your funding is left.
In many cases, residency programs don't really care. ONce you are beyond your IRP, you still get partial funding -- 100% of IME and 50% of DME. Since IME is usually much bigger than DME, this often comes out to 80-85% of funding levels. And many programs are over their cap anyway, so then they just claim someone else with full funding.