You’ve got a couple of options I reckon.
Firstly I would say that you could comfortably say that it is no longer her main residence regardless of whether or not it remains furnished.
If it is unfurnished you could allow a Class C exemption for the first six months.
After the six months, or if it remains furnished, you could consider a discount (up to 100%) under your powers from S13A LGFA 1992 (inserted by S76 LGA2003).
You could consider exemption Class E while she is in hospital if you consider that to be her main home (see above!).
When she moves into the warden aided flat you could consider Class I exemption depending on what care she is going to need. She will have been a relevant absentee as she will have been in a hospital, nursing home etc in the intervening period.
Hope that helps