Please don't worry about rocking the boat or upsetting people - they are the ones mucking you about, not the other way round, and they are probably relying on your good nature and desire not to rock the boat to let them get away with messing you around like this.
If you have had agreement (and have documentation of it) to a flexible working arrangement, this is a permanent change to your terms and conditions, and your employer can't just change their mind.
Having said that, it sounds as though this may be a case of your manager agreeing it without it being checked by his manager, which he may have been required to do - it could well be a case of them agreeing prematurely and now frantically backpedalling and hoping you don't make too much fuss.
None of this is your problem though, and as you said, the notice they have given you of the change of decision is appalling in any case. My guess is they agreed the original proposal prematurely, your manager is probably in trouble for doing so, and they have put forward this similar proposal and are desperately hoping you will agree to it rather than putting your foot down as you are entitled to do.
You could easily challenge their decision to suddenly change their mind, but it sounds as though you would actually be happy with the alternative proposal they are putting forward, as long as you can stay off work longer with your son, spend a bit more time with him and take your time to sort out appropriate childcare.
In that case your best bet is to resolve the issue of not giving enough notice to alter your date of return.
Bearing in mind the ridiculously short notice they gave you about the change in your working arrangements, which meant it would have been impossible for you to give the required 8 weeks notice, and bearing in mind that they are treading extremely dodgy ground agreeing to a flexible working arrangement and then rescinding that agreement, you are in a very strong position.
Write to your boss, say
A) I am giving notice that I would like to delay my return to work until X date. I would therefore like my maternity pay to continue without a break, and the x days annual leave I have booked for x date to x date to be cancelled accordingly. I understand that it is normally required to give notice of a decision to change a return date from maternity leave, however the original date was decided upon based on your agreement to my flexible working application of X date. Now this agreement has been withdrawn at such short notice, obviously I am not in a position to give the usual required notice to alter my return date.
B) With regard to the flexible working arrangement previously agreed, as I am sure you are aware, once a flexible working arrangement is agreed, it becomes a permanent change to my terms and conditions, and once this agreement has been reached and documented you cannot withdraw your agreement as you have done.
I understand you are proposing an alternative arrangement. As it happens this arrangement would suit me, so I am prepared to waive my right to insist on the original agreement remaining in place provided I can extend my maternity leave as detailed above without any requirement to give the usual notice.
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By agreeing to the new proposal without making a fuss you are letting them off the hook a bit, so the least they can do in the circumstances is let you continue your maternity leave without any problem. I would suggest writing in the formal terms I have set out above just so they know you are aware of your rights and the dodgy way they are behaving, but you are prepared to let it go as long as the new arrangement is on your terms. You are being extremely reasonable but it won't hurt for them to get a formal letter so they realise they are lucky not to have more of a fuss.
With any luck, they should let you extend your maternity leave with no trouble at all!
Do that, and see what happens and if there are any problems do come back and we'll sort it out.