New Custom Field Group Warning: 'field IDs do not match the custom table'

We have an existing Meta Box custom-table field group that has been in production for some time.

The custom table was originally created while Auto create table was enabled. As development progressed, we moved to managing the database schema manually and disabled Auto create table.

The current field-group settings are:
Auto create table: Disabled
Storage type: Custom Table

The Meta Box custom field group currently contains:
100 actual data-storage fields

The physical database table currently contains:
100 columns matching the current data-storage field IDs

We manually compared the current Meta Box field IDs against the physical database columns and found no missing current field IDs.

However, after the recent addition of the Edit Table Schema feature, the field group now displays a new warning message:
“100 field IDs do not match the custom table. Update the field IDs to match columns, or update the schema.”

We have flushed object/memcache, but the warning persists.

Our question is:
How should an existing custom table that was originally auto-created, but is now manually managed with Auto Create disabled, be synchronized with the new Builder schema metadata without altering the physical database table?

We would particularly like to avoid enabling Auto Create if doing so could cause Meta Box to alter the existing data types or indexes.

Thank you for any assistance you can provide.