I've not had a problem, but if you're off on a big trip, it's worth just buying new fuel bottle(s) for the occasion. They're not particularly expensive and it saves any potential hassle.
I've come across quite a few people who've had used but totally empty fuel bottles confiscated because there's a very faint whiff of fuel. In S America I was given some weird American liquid - Dr Wotnot's Miracle Peppermint Elixir or something, that took the smell out pretty effectively.
Strictly speaking you should check the airline's regulations and abide by them, but I've never had a problem with clean bottles and stove in the hold. I suspect that if you did declare them, they'd simply take them off you.