Hi loel, I had the same problem and solved it with unregistering the table before loading it with FStringTableRegistry::Get().UnregisterStringTable.
FStringTableRegistry::Get().UnregisterStringTable("MyStrings");
LOCTABLE_FROMFILE_GAME("MyStrings", "MyStrings", "Assets/Strings/MyStringTable.csv");
I use the same ID “MyStrings” for both parameters, because otherwise the localisation dashboard has the same strings under two different namespaces. This also works while having the same csv file as an String Table asset in the editor.
I am still a bit unsure if that is an elegant solution…