All favorites are stored in mIRC.ini.

[chanfolder]
n**=#channel,"description",password,"network",join on connect (1 or blank),minimize on join (1 or blank)

Example:

n27=#Invision,"Invision's Official Channel",,IRCHighway,1

Notice that the password is emtpy because it has no password. And the minimize isn't there because I don't have that checked.

Now, I know you can't change mIRC.ini while it's running, or the changes will be lost when you restart mIRC. I know that you can create a batch file that will make the changes after mIRC closes and that's supposed to work (I've never tried it). There may also be a way to save the mIRC.ini while it's running. If so, I don't know the command.