The version number is the translation version. 4.4 is the latest. You may want to update, but your saves will probably not work with the new version.
I recommend just waiting until you unlock EP2 normally, then update and restore your progress by unlocking it manually in the main menu.
If you really want to update asap, update, then "unlock" EP2 at the main menu and start EP1 again, you'll be given an option to skip to whatever chapter you like. Pick the chapter you were in, then use ctrl to skip the rest of the way back to where you were (if you don't know what chapter you were in, post here and someone will tell you)
If you do end up unlocking EP2 manually before you unlock it normally, make sure to read the bonus "Tea Party" and "????", in that order, after finishing EP1 and before starting EP2. Normally you must read these before unlocking EP2, but unlocking it manually bypasses this.
As for what changed in the two updates from 4.2 to 4.4, IIRC both were general updates to the EP1-4 translation, with the benefit of hindsight from EP5/6/7. I'd imagine they contain things like making hints more (or less) obvious to match the difficulty to the original text, clarifying translations of certain sensitive lines, stuff like that.