Upon revisiting the save, I noticed that I must have messed up after all. I did import the PKM folder successfully and alter the pokedex but in doing so, removed every pokemon from the Hoenn dex I had previously.
To be 100% certain and avoid any further confusion, which are the correct options to select in order to import a folder of PKM files WITHOUT losing any already existing pokemon? Especially the second option is not 100% clear because "cancel" means aborting the entire process, as it does in any software.