There probably aren't any easy answers with this, but my preference lately has been to leave them in, and possibly if it's giving you a bad feeling then it might be a sign of an architectural issue rather than one of just where the code lives (and so maybe something to keep in mind as you continue rather than rectify immediately)
Here's John Carmack on the opposite problem--going from 'too factored' code to inlined code:
http://number-none.com/blow/blog/...9/26/carmack-on-inlined-code.html
The retrospective bit at the top is probably the most relevant, too (emphasis added)
The real enemy addressed by inlining is unexpected dependency and mutation of state, which functional programming solves more directly and completely. However, if you are going to make a lot of state changes, having them all happen inline does have advantages; you should be made constantly aware of the full horror of what you are doing. When it gets to be too much to take, figure out how to factor blocks out into pure functions (and don.t let them slide back into impurity!).