Well, it should always merge the files unless you crash. At least, that's how it's supposed to work. I know that I always have .log for everything except the current log file for each log, which is always .1.log.
If it's not merging correctly and you haven't crashed, then it may be some bug (or perhaps a script) that is preventing the merge. I really don't know because the change in logs doesn't affect me... I can read the current logs just fine through Invision's log viewer.
Although not a "nice" solution, if you have troubles with the logs merging properly, you could have a script that will automatically /hop the channels every few hours or every day or whatever. That /hop should act like a /part and your logs should merge when that happens. (Untested)
