It depends how you are washing them at the moment.
Whilst you suspect thrush, I would always wash at 60+ degrees, and if your nappies can take it, a service wash at 90 degrees would ensure that all the nasties were dead. A good flap on the line on a sunny day will probably do the same job, but I don't expect we'll get many more of those this year!
Do you use fleece liners? They heat up little bottoms, and are sometimes associated with thrush - my ds always gets thrush if we use them. I use cotton liners, so if I suspect thrush (I'm still bf, so if I get it, I act as though he has too) I microwave my liners, which is another way of ensuring that they are nice and sterile.
If it's all gone now, it might just have been the adjustment to the new nappies. I maybe go to extremes because we had repeated bouts of thrush for 6 months (probably not repeated, but never properly got rid of IYKWIM).
If you see the GP, it might be worth mentioning that he 'had' thrush, and get him to prescribe some canesten in case he gets it again - I keep a few spare in the cupboard.
I hope that helps. Any other questions, feel free to ask.