Unless any changes that happen are as a result of your maternity leave, there's nothing you can do from that point of view.
It sounds as though these changes are likely to be happening and your maternity leave is incidental, the only difference being that you are not 'on the spot' to see what's going on.
If your duties will change considerably, will the work you were doing prior to your maternity leave still be done, and if so by who?
Regarding the flexible working application, I can think of several points to make.
Although your manager is asking for it now, you can of course put it in at any time you like, and there are quite strict and tight deadlines for dealing with it. I would imagine they want it now to assist with their planning and reorganisation of roles.
If you don't know what your role is, it's more difficult for you to frame a good flexible working application.
If they are happy to receive it early, they may work out the organisation more or less around the hours you want (although it sounds as though that might be unlikely based on your comments about the senior manager).
If you put in the request before the reorganisation is completed, it could be difficult for them to say it is not possible to accommodate you, as everything is being reorganised anyway.
So if you want to stay, it could be to your advantage to put it in now - you'll have to weigh up those points and decide whether any of the things I've said apply in this case.
With regard to your maternity pay, they have to pay you statutory maternity pay once you have qualified for it, which I am assuming you have. Anything over and above, I would expect the policy to state that they will stop it and may also say that you have to repay some of it, you'll have to check your policy.
If you don't want to go back on June 1st you would need to give your normal (1 month?) notice. So you could resign earlier, but I'd be inclined to keep my options open longer just in case.
If you're getting wound up just thinking about it and hate the direction it's taking, maybe considering a move might be the best option anyway?