I would be very surprised if you had (inadvertantly) "forced" **_help.txt setting changes into any SH3Cmdr Cfg files because the **_help files are literally straight text files - in other words there's no "hook" for SH3Cmdr to make individual line changes. So the only way SH3Cmdr could change the help files is if full copies existed in its Date, Flotilla, Random or U-boat folder structures.
So do a search of your SH3Cmdr installation for en_help.txt and de_help.txt files and delete if found.
This is in addition to doing the above check I've outlined.
If no files are found through either check, then regardless of how it seems, you will need to look beyond SH3Cmdr as it could not possibly be the culprit (as every file it changes is backed up, so no file in the !BACKUP folder means no changes were made to that file by SH3Cmdr).
If you run multiple installations of SH3, you may also like to check whether the "wrong" GWX help files are the same as the ones in any of your other SH3 installations. That may provide some insight into how the wrong files got into your GWX installation.
FYI the correct GWX help file should contain the following "pages":
# NAVIGATION CONTROLS
# STATION CONTROLS
# OTHER CONTROLS
# ENEMIES OF GERMANY
# RESUPPLY INFO
# UBOATs & DISTANCE INFO
# FLOTILLA NEWS I
# FLOTILLA NEWS II
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