Clear `pending_deletion` flag on Env reset

If we mark some node as 'pending_deletion' and then reset the environment,
the node will have both 'pending_deletion' and 'pending_addition' flags.

Since now, the reset environment process clears 'pending_deletion` flag.

Change-Id: I72182e5bdbe07a399fd16f71559cacf599d7a9a4
Closes-Bug: #1310604
Merge "Clear `pending_deletion` flag on Env reset"