Chapter 31 (now changed from Voc-Rehab to Veteran-Readiness & Employment Program) would be very difficult to get approved twice: once for undergrad, once for grad school. The purpose behind the program is to present itself as an employment track and not an education track (although all of us use it for school).
To be approved, I assume you applied on e-benefits and scheduled a phone appointment with your present counselor. He/She is correct that you can switch over to Chapter 31 for the remainder of your undergrad, but I highly discourage this. You will need to finish an
Individual Written Rehabilitation Plan (IWRP) once your counselor determines you are approved for the remainder of your "current" education. The IWRP would only state that your end goal is employment upon graduation of undergrad. It cannot state that the track is merely a pre-req for physical therapy school and as a result the program will continue to cover your schooling. Since the schooling is in a different location, you would have to re-apply for the program and convince the new counselor as to why you need the assistance a "second" time since it is not related to the worsening of your disability claims. Also (and this is tricky and sensitive), if you cross-over from GI Bill to Chapter 31 and graduate, for every day you used Chapter 31, it takes away from your GI Bill. Since you stated your GI Bill would have ran out by the time you graduate, you would have forfeited the remainder of you GI Bill upon graduating with Chapter 31. AND (sadly) if you graduate with Chapter 31, that is the end of it. Chances of a second trial with Chapter 31 is out the window.
The truth is, you can only use 48-months of total education benefits with the GI Bill + VR&E combined (36 months of GI Bill + 12 month extension with VR&E). However, an exception to this rule is if you qualify of having a
serious employment handicap (SEH) which is that your disabilities are so severe and aggravated, that you need to do a "change-of-career" in order to better suit the needs of yourself and your dependence (ie go from undergrad to physical therapy). If you qualify for this, you can use VR&E beyond the 48 month rule. However, this is very very difficult to do for those pursuing higher education ( I was turned down twice myself before finally getting the approval for pharmacy school).
To sum it all up, it is very difficult to be re-approved for VR&E if you use it in undergrad. You not only forfeit the remainder of your GI Bill, but your shot of using VR&E at its full capacity a second-time is diminished. The best option is to save at least ONE DAY of your GI Bill and then apply for VR&E with your reasonings for the higher education (ie disability getting worse and cannot work with current credentials despite getting an undergrad degree). If you save at least 1 day of current GI Bill, AND you get approved for your VR&E, you will get paid at the higher housing rate provided by your GI Bill (VR&E has a very low monthly housing stipend). Should you be denied VR&E initially, you can reclaim the paperwork and appeal. Should you eventually get accepted, they will back-pay you from the day you applied at the beginning of school rather than the day you got accepted in the VR&E program. However, without that SEH sticker on your application, you will only be approved for 12 months of VR&E for physical therapy, not the full time in school (remember, 48-month rule).
This is a lot of information but I hope it is clear enough to at least get your decision started on how to approach this. Unfortunately, many counselors are uneducated on the new rules, or are set in their old ways and will deny anyone who already has criteria (degree) and not give them a second thought. It's a delicate process and is much harder for healthcare professionals to get approved than anyone else. If you have additional questions don't be afraid to ask. It's cutthroat with certain counselors but there is a certain way to approach the process without getting turned away.