This is not a variant spelling—that is, not one you could use if you chose to and be correct. The last non-standard spelling the OED records is this one, in 1612: 'By these two blessings (to wit) the sunne & raine meaning al other earthly benefits whatsoever, by the figure synechdoche.' If you write'al', or 'sunne', or 'raine', by all means write'synechdoche', but don't expect to get it by living proof-readers.
There's another instance of this from 1551; while in a 1548 source we find 'They imagyne a Sinecdoch to be in thys worde' and 'The subtyll cauillacyons, whereby they fayne Sinecdochine'. That was how they spelt then; it isn't now.