I had a loss of the Transcendence mutiplier, but this could be related to the update from 0.5 to 0.6. It frustrated me a bit.
I was pleased to notice the changes in the new version.
However, when I play the game in the browser, it is still unclear to me when my progress is actually saved or when it was last saved.
I've had the problem several times where I've made progress but it hasn't been saved, so the game can't be continued from the point where I actually finished it. Perhaps a manual save option would also be useful.