Force the last checkpoint to be saved.

We throttle the checkpoint if it's less than 1 second, but this could
lead to the last checkpoint not being saved, reset the checkpoint time
to make sure the last checkpoint will be saved.

Also improved logging when payload size mismatch happens.

Fixes: 122628007
Test: cancel update during postinstall, resume the update

Change-Id: Ia38e036ea81c9a09a16a3e589983e675ab2982cc