Thank you for the answer Kvellen. Unfortunately, it did not work for me, as it only made savegames from before the patch appear (which were all the way back into Act 2).
However, out of frustration, I decided to delve into the savegame files to see what I could find, and I believe I've found the solution:
Go to your Pillars of Eternity 1 Saved Game directory. (C:\Users\"username"\Saved Games\Pillars of Eternity)
Open the "gamecomplete.savegame" file in WinRAR.
Look for the file "saveinfo.xml" in the archive and open it in Notepad.
Find the following string and simply change value="3" to value="2":
Save "saveinfo.xml" in the archive, and then select "Yes" when WinRAR asks if you wish to update it in the archive.
The completed Pillars of Eternity 1 save file should now appear when you are prompted to import a save into Deadfire, regardless of which patch the game was completed on.
Hope this helps others who are in the same boat.