Wondering out loud, with the hope someone who has tried this will respond...
After one gets past the point of running a pair of projects in AXv3 (LeftJustified and UpgradeColumnList) and the AOS is shut down (presumably for the last time), there appears to be no reason to retain any of the indices in the schema. Removal of the indices would greatly speed up the migration process.
* The v3-to-v4 DB Upgrade Preparation Tool uses SQL batch loads to transfer files output to disk into a blank destination database.
* The Synchronize step on the v5 checklist will create indices as needed.
Would it be okay to drop all the indices prior to running the v3-to-v4 DB Upgrade Preparation Tool and let the Synchronize step recreate them?