You shouldn't have to change the .rsd or sm_factions reference unless you're trying to reference the logos on sharedpage_00.tga and stratpage_03.tga, if you are I suspect easier way would be to cut and paste them over factions that you're not using on sharedpage_01.tga and stratpage_02.tga

I don't know which file gives the pop up bar logo but I've got it displaying the ammended logo just by altering the .tga's.

I think (must remember to write this down properly the next time I do it!) that the only ones I changed were: replacing tga's for relevant faction in
data\menu\symbols\FE_buttons_24
data\menu\symbols\FE_buttons_48
data\loading_screen\symbols

and pasting in new logo on top of old one within
sharedpage_01.tga and stratpage_02.tga
both in data\UI\culture\interface
If you've pasted new logo over the factions that you're ammending you shouldn't have to change the sm_factions reference.

Only quirk we've found to that is in RTW sm_factions dacia has:
small_logo_index 263
if you use that reference with BI .rsd files and sharedpage_01 you get the swimming logo in diplomacy screen, changing number to 264 gets expected logo back.