I don't THINK you need worry too much about the drop in your girlfriend's earnings as a result of her presently being on Statutory Maternity Leave,since the Home Office is bound to be well aware that this is likely to be the case with women in her situation. What IS important, though, is that the two of you have lived together ... in the same way as a married couple would ... throughout the qualifying period for her permanent residency (ILR) and, that your JOINT income plus savings are adequate for your basic needs ... and those of *dependent children ... after payment of rent.
*Which brings me to your mention of [household] income having been further depleted by childcare costs, etc; what does the ETC. entail ... is it necessary outlay? Can it be pared-down in any way, if non-essential?
It may BE, that I'M possibly a bit "out of my depth in trying to advise you properly. And so, to ease your mind more fully, I believe it would be worth your while waiting for others' responses to your post. Good Luck!