I've never tried this but based on the behavior of other config stuff here's what I'm thinking:
I'm pretty sure we're talking about changing it in a conf file in which case upon restart Splunk will not know about the old location and will just see that the accelerations don't exist in the new location and therefore need to be built. The acceleration files in the old location will persist because there will be no task to clean them up. If there is a way to move (not just change) the location in the UI or REST or CLI, then that's the best bet for having splunk handle the movement of the respective files - but I don't think such a thing exists.
I would suggest stopping the acceleration, seeing if that cleans up the respective files, then implement your change.
Does that jive with what you were asking or did I misunderstand? Let me know because obviously I answered without doing research first.
