Colleges operating or planning these deals are urgently considering the impact of Further Education Funding Council guidelines which categorise some forms of sixth-form franchising as illegal.
David Bunch, principal of North Derbyshire College, which runs two sixth forms in local schools, admitted that "ceasing the current arrangements" was one option being considered.
If that happened, around 200 sixth-formers in the two schools would have to go elsewhere, and might have to move out of school to one of the college's own sites.
Carshalton College, Surrey, which is due to franchise a sixth form at a neighbouring school from September, says that 86 students enrolled for next year might have to be offered other options.
Both partners say they are optimistic the arrangement will go ahead. Failure would embarrass Carshalton principal Dr David Watkins, who was a member of the FEFC franchising working party which issued the guidance.
Both stress closure would be a "worst case scenario", and aim to find ways to move within the guidelines. Both said students would stay the top priority.
Long-awaited advice from the FEFC covering all forms of franchises said lawyers believed that a school sixth form, funded through a college but staffed entirely by a school, would be illegal.
Funding chiefs said they had "no evidence that such arrangements are being made", but told principals engaged in such schemes to contact them. Sixth-form franchises in which college staff carry out all or part of the teaching are more likely to get FEFC approval.
Mr Bunch, whose college launched its links with schools in 1993, admitted the sixth forms included "very small numbers of college staff". He said: "It looks as if we are going to have to at the very least adjust and indeed we may have to look at ceasing the current arrangements."
Expectations that the FEFC guidance would effectively rule out all sixth-form franchising have not been fulfilled.