My way you'd still have to merge your changes back to the trunk, so yours should be correct. What you're doing should work. I can't think of any reason you should be losing your changes.
It's amazing how quickly you forget this stuff when you don't use it every day any more.[1] Oh, and you should be using the [link|http://ximbiot.com/cvs/manual/cvs-1.12.13/cvs.html|Cerderqvist]. Specifically looking at the section on [link|http://ximbiot.com/cvs/manual/cvs-1.12.13/cvs_5.html#SEC56|branching and merging]. Actually the link at the top says you should be using the [link|http://ximbiot.com/cvs/wiki/|CVS Wiki]. I'm more familiar with the Cerderqvist though. Visual memory helps.
[1] And when the last time you used it, you were using a GUI.[2]
[2] Yeah, I used tkCVS. You gonna make something of it?