To my knowledge, when mIRC is closed, any manual changes made to the active .ini files (mirc.ini, servers.ini, control.ini, etc.) will be over-written.
If you want to make changes to those files, either do so while mIRC is closed, or use mIRC's internal functions to make the changes. Most (if not all) changes that you would want to make can be made using mIRC's internal functions. These functions are, generally, available through the Options section (Alt + o)