TOTALCMD.INC is not language specific and has to be placed in TC's program folder.
There can be a wcmd_mylanguage.inc file in the language directory with the translation of the legend for the command strings used for example in the Choose command dialog (cm_CommandBrowser).
If you have customized totalcmd.inc it shall still have the name of totalcmd.inc - you can prevent it from being overwritten by the installer by marking it as read-only - but then of course you won't get any new commands that might have been introduced since the last version of TC.
So regarding customized totalcmd.inc there is no other way than to keep a backup that you can merge with the new totalcmd.inc that is overwriting the old one by the installer.
It is only the purely language specific files that you can give a customized name to keep them from being overwritten - those files are wcmd_xx_language.lng, wcmd_xx_language.mnu, wcmd_xx_language.inc and wcmd_xx_language.ini
for example:
wcmd_pm_dan.lng, wcmd_pm_dan.mnu, wcmd_pm_dan.inc and wcmd_pm_dan.ini
They have to start with wcmd_ and end with _lng in the filename part in order to work properly - where lng is the 2 or 3 digit code for your language (eng, deu, dan, cz, sk etc).
See
http://www.ghisler.ch/wiki/index.php/Backup
.