My dd has had thrush. Did your HV/doctor give you a cream for it, it needs to be treated. Make sure you wash everything at 60 (including cloth wipes etc). I blitzed my nappies at 90 but you may not want to do this. I also stopped using fleece liners for a while to keep the temperature down, this seemed to do the trick and I reintroduced them after a few weeks.
Yes I've got daktarin to put on it twice a day and I've gone back to paper flushable liners for now. Feel bad as I started using the fleece liners to try to improve her nappy rash not make it 100 times worse!!
Don't feel bad, nappy rash has a mind of its own I'm sure. She probably had the thrush before you used the liners. I would definately try them again when it's cleared, you can wash fleece at a high temp.