I asked for recreating indices because I expected we would need to change the column type for uuid from BLOB to TEXT/VARCHAR(36). Sqlite3 has limited support for altering tables, and often you have to perform a dance of copying tables, and this dance requires one to recreate all relevant indices because it's strictly speaking a new table. However, the uuid column has been a VARCHAR(36) since the beginning by mistake, and luckily we don't seem to have suffered from any data loss or corruption due to this mistake. The current indices can be found in the definition of Builder_db.migrate.
I prefer to not rely on parts of Builder_db.Rep that might change (like uuid) in migration scripts. Things I consider safe is id, fpath and cstruct.
Remember to also update the db version in db/builder_db.ml as well :-)