Hi,
Just wanted to say it will come good eventuall so stick with it... As I'm learning from bitter experience - these transitions can be bumpy rides for a couple of weeks but they do eventually iron out. We've just gone through the 3 to 2 nap switch at 7 months so I can relate to your bad day(s)!!!
Could be a few things:
You may be suffering from the 45 minute nap monster. Some say this is over tiredness, others say this is the baby not being quite tired enough. I've never really come to a complete conclusion myself, but you might want to read the sticky posts on 45 minute naps and see if you recognise anything in Lily. Probably a good idea to watch her cues really really closely for a couple of days, could be that you've stretched too far on her A times, or not quite stretched far enough. I'm really guilty of following the clock rather than DS's cues during transitions and have to remind myself to slow down a bit and not push him too far. You may just need to tweak her A times slightly to get the right result...
Or it could just be a mantra cry - are you hanging back to check if she really needs your help? She may be able to resettle herself, and sometimes going in and trying PUPD and shh pat makes it worse (I can really relate to that!)
Wake to sleep is a good tool if you can get the timing right, and it may get her over that 45 minute bump. Be careful not to rouse her too much, in our case, just opening the door of DS' bedroom is enough to get that "sigh" or "heartsluff" as Tracy calls it in her books. I was going in at 35 mins which helped us, but I think all babies are different.
Anyway, hang in there - it will get better.
xxx