Hi,
I have heard that all emails are not archived during the archiving schedule ... but for indexing, it sounds really odd. In Enterprise Vault 10, when you start rebuilding/updating/verifying/synchronizing an index volume, all the operations are queued and are processed based on the index service settings and the schedule in the Index Administration Task.
In EV 9, we recommend to rebuild in small groups at the time so the EV server doesn't get stuck with indexing operations. In this case, the index operations will complete regardless of any schedule.
If what you want is to complete the index synchronization in a certain time, you need to consider the size of the archive, storage, network speed, SQL fragmentation, etc.
If you are running EV 10, you can change the schedule of the Index Administration Task to run after business hours.
I hope this helps.