Difference between disable/delete during synchronization
Synchronization operation first reads all options from the configured database table and compares them to existing option in custom field configuration. If a value is deleted from DB, thats where disable/delete options comes into play.
If delete is selected and option has never used for an issue, synchronization operation deletes the option.
If delete is selected but option has already used for an issue, synchronization operation only disables the option.
If delete is not selected, option is disabled independent of whether it is used for an issue or not.