I think there are a lot of things which might have an influence. The first message for example is displayed if there is a section access included and any data-reduction took place. Therefore you may look if this is the case and if - if there were any changes to the user / machine / loaded data which might now lead to the data-reduction. Just for testing you may disable/remove the section access to check if the lost of the application continuous and/or to check if the issue remained if you always reload the application before saving them.
Whereby even by using section access and if there were any data-reductions it should not happens. Therefore there is probably more which caused in combination this issue, for example:
enabling of auto-saving
any adjusting within the easter egg (independent of it - backup the settings.ini and then remove it to start the next time with the default-values)
not using a ntfs storage else any kind of nas
new/changed security tools / group policies or similar stuff (beside the QV upgrade were there other changes in the environment ?)
not enough storage space
conflicts between the creating release and the new release
use of prj-folders
the app is locked by any other user / process
Does it happens only to you and your machine or are others also effected? Before looking on any point a re-installation of QlikView is quickly done and excludes that there were anything wrong with the previous installation.