No problem at all :) And yes, you can just continue on from your last save like normal.
Note that sometimes the Itch app does this weird thing where it deletes your manual saves so if you want them 100% safe you should back them up beforehand (downloading the new version and extracting it manually doesn't have this problem) but if you don't care too much then you can just click the "A" at the bottom of the screen, to the left of the page numbers, and load an Autosave. Autosaves happen every time you sleep.