Ordinary database engine is deprecated but there is no simple mean to change database engine to Atomic for existing databases.

Possible options:
- ALTER DATABASE MODIFY ENGINE query.
- Flag that triggers migration at ClickHouse startup.

The latter should be easier to implement. 

if (part->info.level > 0)
        {
            ++unexpected_parts_nonnew;
            unexpected_parts_nonnew_rows += part->rows_count;
        }
    }
    const UInt64 parts_to_fetch_blocks = std::accumulate(parts_to_fetch.cbegin(), parts_to_fetch.cend(), 0,
        [&](UInt64 acc, const String& part_name)
        {
            if (const auto part_info = MergeTreePartInfo::tryParsePartName(part_name, format_version))
                return acc + part_info->getBlocksCount();
            LOG_ERROR(log, "Unexpected part name: {}", part_name);
            return acc;
        });
    /** We can automatically synchronize data,
      *  if the ratio of the total number of errors to the total number of parts (minimum - on the local filesystem or in ZK)
      *  is no more than some threshold (for example 50%).
      *
      * A large ratio of mismatches in the data on the filesystem and the expected data
      *  may indicate a configuration error (the server accidentally connected as a replica not from right shard).
      * In this case, the protection mechanism does not allow the server to start.
      */
    UInt64 total_rows_on_filesystem = 0;
    for (const auto & part : parts)
        total_rows_on_filesystem += part->rows_count;
    const auto storage_settings_ptr = getSettings();
    bool insane = uncovered_unexpected_parts_rows > total_rows_on_filesystem * storage_settings_ptr->replicated_max_ratio_of_wrong_parts;
    constexpr const char * sanity_report_fmt = "The local set of parts of table {} doesn't look like the set of parts in ZooKeeper: "
                                               "{} rows of {} total rows in filesystem are suspicious. "
                                               "There are {} uncovered unexpected parts with {} rows ({} of them is not just-written with {} rows), "