I think the best move would be to contact local conservation groups to see if they have any advice. Presumably the council has granted planning permission for the building works and they might have already considered the wild flowers. If not, the conservation group could get involved to stage a rescue. If wild orchids are involved, they can probably pressure the council to allow them access.
Digging up wild flowers is illegal and if you just head in there with a spade, you could be liable for prosecution, however good your intentions are.