My understanding is that red lion on yellow background refers to
Holland, one of the provinces united later into Netherlands, which could be available as a single-province revolter state (is it?).
Dutch Republic (=United Provinces) should already start in 1580s (the very beginning) with yellow lion on red background and I think year 1648 (final recognition) didn't have an effect on their national symbols. I'd say the difference lies in the size of the country (one province vs. united seven provinces) rather than being simply timeline-related.
EDIT: OK, at last sight, I read something that may point to this inversion (and
make my information above invalid):
After the completion of its forming in 1584 the Republic of the Seven United Provinces used as its arms: Or a crowned lion Gules armed and langued Azure, holding in his dexter paw a sword and in the sinister paw seven arrows tight together Azure. The colours of this version where derived from the most important of the seven provinces, the county of Holland (its arms are still in use since being adopted by the counts of Holland in ca 1198) After ca 1668 the colours where reversed and the arms became Gules a crowned lion Or armed and langued Azure holding in his dexter paw a sword Argent hilted Or and in the sinister paw seven arrows Argent pointed and tight together Or.
I find it really hard to decipher those heraldic colours but it seems to refer just to that case. Again, Wikipedia.