Hello!
I'm not quite sure what you mean by "mixed up" - all of the pages should load properly. Is any data from your project missing?
Note that this latest release did change the way sub-pages work - now, duplicating Sub-pages won't link to the original pages anymore (i.e. copying a sub-page and pasting it won't create two Sub-Page cards that point to the same sub-page). Instead, duplicating Sub-Page cards will just create new, blank Sub-Pages - you would use the Link Card instead to link between pages, as this is more reliable and it doesn't really make sense to have sub-pages do what Link Cards also do (but less uniformly). This change also applies to existing projects loaded up in 0.8 Alpha 5 as well.
Automatic backups would be good to re-implement - I've forgotten to add that to the todo list, but I'll add that now.