I would edit the OS 3.1.4 prefs programs with a binary capable editor (for example CED), and replace the LOCALE:Sys strings with LOCALE:314 and put OS 3.1.4 locales there, and keep OS 3.9 locales in LOCALE:Sys, and hence have both working. Or vice versa.
Most glaring problem that I am aware of is the IPrefs of OS 3.1.4 and 3.9 support different, incompatible supersets of IPrefs of OS 3.1.