In-Portal is modular system, where modules can be installed in 2 ways:
- during initial system installation
- afterwards from Modules list
It turns out, that module installation imports language pack with "overwrite" option enabled which does no harm when you have empty database or modules don't have overlapping phrases in them. However if you install module on a working project, then it overwrites contents of Language table, including any custom e-mail template design that might have been there.
I propose that when installing module separately from main website installation we do language pack upgrade (no overwrite) as we're doing right now when module is upgraded to next version.