Penyrheol comprehensive in Swansea was reduced to rubble after a blaze ripped through the building last March, destroying pupil's coursework and a library.
A 17-year-old was later charged with deliberately starting the fire, which caused pound;8 million pounds worth of damage.
Teaching staff were praised for working extra hours in difficult conditions to recover from the incident, working from makeshift classrooms and leisure centres during the exam season.
But a deepening row over TLRs is reaching crisis point at the school, according to the National Union of Teachers Cymru. Members staged a one-day strike before Christmas over the "complete dismissal" of negotiations by the governing body.
David Evans, NUT Wales secretary, said the situation had become so bad at the school that some of the 17 teachers affected have voted with their feet and left.
Mr Evans said nine of his members have lost close to pound;20,000 but the headteacher, Alan Tootill, is unwilling to back down over his own restructuring plans. Mr Evans said:"At Penyrheol, many staff feel they have suffered a metaphorical slap in the face. This has added to the stress of what has already been a very difficult time.
"The strike at Penyrheol has been in response to high-handed and insensitive treatment of committed and hard-working teachers.
"The more the head digs his feet in, the more damaging is the effect to staff morale." The introduction of the new TLR structure, which came into force in Wales last March, went more smoothly than expected, with only isolated disputes and strike action.
Some say staff who have lost TLRs should not have been doing the extra duties in the first place. But the union said at the end of last year some teachers had lost up to pound;5,600 in the restructuring.
Many disputes seem to be concentrated around Swansea, including Gowerton and Cefn Hengoed comprehensive schools.
Penyrheol head AlanJTootill said: "I have met twice with the NUT. The vice-chair of the governing body was present the second time. We want to resolve the dispute, but strike action is not a reasonable way to negotiate."