Are/were you or your DH self employed? Has your household income changed since the 2nd year? Did you get married after your DS finished the 2nd year so now your DH's income has been added to your income?
As PPs keep saying, the 3rd year loan is only reduced by a small amount because it only covers 9 months instead of 12 months. Unless he is an NHS bursary student eg medicine/dentistry, which has different funding?
You would have to have a household income of around £60k for your DS to only get £1k a term.
If the loan was reduced in the 3rd year because your household income is high enough that you are expected to top it up and you didn't, I think morally, the debt partly your fault. Is the issue that you can't afford to help him out but his loan was based on his DSF's income? Although why didn't he speak up sooner and ask for help or apply for a university hardship grant or look for work? You can check for yourself that it is correct using the student finance calculator:
www.gov.uk/student-finance-calculator
He hasn't included his DF's (your ex) income too, has he? Were either you or your DH self employed so the loan is based on your most recent tax return (ie over a year ago) or did your income reduce after the application was made? If so, if your income is significantly less now, SFE will recalculate the loan on your current income. The deadline is looming though (I think it is 31 May). Had he ben overpaid in previous years because your income went up after the application so SFE reduced this year's loan to take back the overpayment?
I'm not sure if it is too late now his exams have finished but has he asked the university if he is eligible for a university hardship grant or loan?
Are you sure your DS is telling the truth about the loan? If he correctly received £6k less this year, you are expected by the government to top up the loan. I do understand that you can't afford to but, nevertheless, his debt is partly down to you and your DH in that case. Are you sure he isn't using the slightly reduced loan in the final term to muddy the waters and hide the real reason for the debt ie he got less funding this year but not £6k less? I would be concerned, coupled with his depression, that the money was spent on something else eg drugs, drinking, gambling.
I do empathise with you if the reason is you were supposed to top up the loan and you couldn't afford to. Lots of parents are in that position. Please don't think I am being judgey or critical of you or your DS, I am just trying to be pragmatic to help you sort this out.
If you are concerned that your DS may have failed his degree, have you discussed with him whether he applied for mitigating circumstances to be taken into account because of his depression and financial stresses? The deadline may have passed for applying now but sometimes late applications can be allowed if the student has mental health issues that meant they couldn't cope with dealing with the mitigating circumstances application. You might get better advice on the HIgher Education board.