When you restore an application from a previous backup, the following elements are NOT restored, which can lead to significant manually updates being required to fully get the app back to the previous state:

1.All Report Restrict Visibility settings are lost - any reports that were previously set to viewable by all users revert to just 'Only Me'

2. All hidden columns on reports become visible after restore

3. All Role definitions are lost

Whilst the last one is quite readily fixed manually as most role hierarchies are relatively simplistic, the first 2 can create a significant workload given the number of reports produced for anything other than a very basic app.  

Has anyone else come across this shortfall and come up with workarounds to make good deficiencies that really should be fixed in the base product?