Where and how to I clear the cache for the kernel/user on the N900?

I can see that it exists, in that the device seems to ignore some changes I make to settings files, and I can scroll through my previous command line inputs in X-Terminal.

If you want to remove the command line history, this would usually be

history -c

For "ignores some changes to settings files I make" you should include an example of which file you've tried to change.

After changing settings you'll need to restart the app that uses them. This will always happen through a reboot, but many apps can just be closed and started again. In a few cases one needs to run a script to move the settings from where they are edited into the live config, but those cases should say so in the instructions on how to change them.

A value of 1 frees the pagecache, 2 frees dentries and inodes and 3 all of the above.

This have nothing to do with kernel cache.

Previous command line inputs in X-Terminal are history saved by your shell. Assuming you use the default shell, there is no history command. Try something like:

rm ~/ash_history
exit


The issue with settings is that some programs read configuration only when they start, or when they get a command to reread configuration. If you describe the specific settings you change, you might get help in activating the changes immediately.