Hello and thank you for playing the game.
As for the progression reset between the updates, it is a problem with the engine:
Long story short, technically, you could just manually copy save files from update A to update B, but this surely will result in some weird/ unexpected glitches.
The main problem here is that the engine doesn't recognize any changes made into the scene between the two different versions of the game. Basically, all the settings of the currently playing scene (when the character portraits are shown, how the text is displayed, when the scene ends) are all tied to the save file. So, for example: If you save the game in the last scene of build A, which ends at the line XYZ, then if you reload this save file in build B (which should continue this scene after line XYZ), the game will still end up at line XYZ. I know, it sucks.
That's why I programmed the "Continue from specific a point in the game" option, which can be found after selecting "New Game" from the main menu. From there, you can easily jump back to the most important story points and continue from there.