Persist permission state for updated apps synchronously.

Because if we lose the changes, an updated app won't be reconsidered for
new install permissions.

Fixes: 221899913
Test: presubmit
Change-Id: Ib82189b07cf4dfd132be37fb19843d770e871f8c
Merged-In: Ib82189b07cf4dfd132be37fb19843d770e871f8c