Its been really difficult to make suggestions coz you haven't really said what it is that you do....
One of the first boundaries that I set and think is perhaps where you are struggling is with the upstairs rule. You are absolutely right that once you are upstairs, you should stay there. By going back downstairs after the bath she's confused about what it is that you are doing.
With DS, once we're upstairs, he never comes down (maybe a couple of exceptions when he's accidentally had a late nap in the car but very exceptional!). I do let him watch telly, but only Cbeebies, and that finishes at 7 so is a really good indicator to him that its time to go upstairs, have bath, story, bottle and bed.
What time are you giving her the bath, how long do you spend in it? What time are you aiming for her to go to bed and when does her dad get home? It would be nice to have a routine that incorpates her dad too wouldn't it?
I actually don't see a problem with sucking the flannel if she's going in a big bath, based on the fact that anything in there is going to be so massively diluted its not going to do her any harm at all - I can't stop DS drinking the bathwater and he's perfectly fine!
If it was a small bath still then I can see your point but at 13 months I imagine she will be splashing and crawling about in a decent amount of water in the bath?
And to pull you up on something, the routine doesn't go out of the window - what you do is the routine...its the only thing she knows and she is confused about whether its play time or bed time. You aim is to fill every one of her senses with 'bedtime' e.g. dark, quiet calm voices, warm, full tummy (bedtime milk drink), cuddles, teddy bear, story time etc etc.
Where in your bedtime routine do you come back downstairs, put on the playstation (or whatever) before heading back up stairs and having someone expecting you to fall straight to sleep?!!
Oh my, but wouldn't it be nice if someone did run as a bath, give us a warm milky drink, read a story, quick cuddle (with no funny business expected), then tucked us into bed - I'd go to sleep straight away!!! LOL!
Sorry, I've really rambled...will post anyway...