Seeing as absolutely nothing carries over anyway, treating them as separate stand alone games seems like the simplest solution. I mean what's the point in mushing them together when there's really nothing that carries over between episodes anyway? Nevermind how long each episode stands. Back in the 'episodic' days of RMXP, some folks would let out games were that were no more than 15 minutes long and had no gameplay to them, at all (ScriptKitty's Akasha Seal, for example). People were okay with it. You can just compile everything into a single game afterward when you're done (Volrath and ArtBane's Master of the Wind series, which was at first episodic then combined).
If you wanted something expandable, the easiest solution is probably to keep the game unencrypted. Have something that logs changes like SVN so you know what's being changed between updates and upload only the relevant files every update to reduce file size. Updating would be as simple as copying and pasting the update folder into the main game folder. It's not the cleanest solution ever, mind you, but I'm running on the assumption here that you don't have any other fancy scripts to do the job for you on hand.
Also, at least this has proven true in XP and older versions, it's easy to carry saves over to new games. When making the second game, build it over the first one. Delete the resources you don't need (all the map events, maps you no longer need, sprites you no longer need, etc) and make sure you don't use any of the database slots (characters, variables, switches, etc) that you may have used in the old one. This ensures that all the old player data recorded in the first game are protected and the game will still read whatever was on them when it tries to load it.
Want your party from the first game to show up again with their items and levels intact? No problem. You want your recorded choices in the first game to affect the plot of the second? Easy. Did you set a switch on the first game so if you loaded your old save from the first game to unlock a cool secret character on the second? Also possible. Just have players copy the save data on the first game and paste it into the folder of the second.