DD is 15 and autistic (diagnosed a year ago). She has shutdowns just as you describe. All fell apart in Y10 (pre-diagnosis) with her doing lots of hiding in a toilet and texting us saying "I just can't".
She then crashed into burnout a year ago and her attendance slumped hugely. Got signed off completely by the GP in late June. They've now agreed to her going back doing just 3 GCSEs.
School have been pretty supportive, mostly of us just contacting the absence people every day saying "she won't be in today" or "we're bringing her in at lunch (or whatever). We got to Stage 2 of the absence procedures - once you miss a certain amount of school you get letters. They called to warn us they were coming. At stage 3 you get invited to a meeting with the local authority which we were almost looking forward to as it would give us a chance to speak to someone and ask for help? For some reason we never got the stage 3 one - her attendance was definitely bad enough to warrant it.
I applied for the EHCN assessment before the school holidays (just did it myself through the LA website) and got refused because they sad school should be able to provide a reduced timetable which at the time wasn't being offered. I think as a result of that application they then agreed to the much reduced timetable.
My number one advice is that you know your child (and you sound like you're doing a great job). Make it clear he's not going to go to detention for missing a class because he's overwhelmed. Insist that they're failing him in their duty of care as it's clear he's not coping.
We were on the NHS waiting list for an autism assessment but ended up going privately as we couldn't wait. If you can't afford that I'd recommend going down the Right To Choose pathway as it's much quicker How to request an autism assessment It will still take some months but you'll be waiting years and years otherwise.
Also, DDs school gave her support without a diagnosis (mainly access to a Regulation Room she could go to when class got too much). There were certain things that were too hard - for a bit in Y9 she just couldn't cope with PE so we told them we were going to just pick her up and take her out of school during those lessons as it was clear being there was bad for her mental health. Same for registration - we take her in for the end of registration every day.
A diagnosis helped her to understand that her brain works a bit differently (we're big fans of 'different, not broken'). In our family DH has also just received a diagnosis, and we're going privately for as assessment for DD1 (17) who was on the list for one through Right To Choose but the wheels are coming off there as well and we feel we can't wait. The journey of understanding how everyone works has been long and painful (and we're nowhere near there), but diagnoses have helped us access support (the Access Card has been amazing for DD2 to keep doing the things she wants to do, and I've applied for DLA for her because she can't get a job, and because caring for her takes additional time and money that wouldn't be a thing if it weren't for her diagnosis).
There's a lot she can't do - she gets overwhelmed easily - but understanding what's going on has allowed us to try and get a balance of getting her the support she needs (same for DH and DD1 soon).
I'm currently reapplying for an EHCN assessment, as that would allow her to stay in funded education longer. I'm trying to get an Occupational Therapy assessment and seeing if I can get the Local Authority to pay for it - if she was in a wheelchair they'd do all the necessary assessments and adjustments - I can't see why that's different just because her issues are social/sensory/neuro?
Happy to chat if you want to message me xx