manual transfer fails with table does not exist I performed a manual transfer of data manually (zip up the dir and rsync'ed it over. I moved the members.ibd (the only .ibd file) to a save place, extracted and then replaced members.ibd with the original.
But only the members table can be found.

The rest of the tables are broken.

error:

mysql&gt; select * from transactions;
ERROR 1146 (42S02): Table 'nyc_primary.transactions' doesn't exist


I can see the tables:

mysql&gt; show tables;
+---------------------------+
| Tables_in_nyc_primary     |
+---------------------------+
| accounting                |
| domains                   |
| members                   |
| phpbb_acl_groups          |
| phpbb_acl_options         |
| phpbb_acl_roles           |
| phpbb_acl_roles_data      |
| phpbb_acl_users           |
| phpbb_attachments         |
| phpbb_banlist             |
| phpbb_bbcodes             |
| phpbb_bookmarks           |
| phpbb_bots                |
| phpbb_config              |
| phpbb_config_text         |
| phpbb_confirm             |
| phpbb_disallow            |
| phpbb_drafts              |
| phpbb_ext                 |
| phpbb_extension_groups    |
| phpbb_extensions          |
| phpbb_forums              |
| phpbb_forums_access       |
| phpbb_forums_track        |
| phpbb_forums_watch        |
| phpbb_groups              |
| phpbb_icons               |
| phpbb_lang                |
| phpbb_log                 |
| phpbb_login_attempts      |
| phpbb_migrations          |
| phpbb_moderator_cache     |
| phpbb_modules             |
| phpbb_notification_types  |
| phpbb_notifications       |
| phpbb_oauth_accounts      |
| phpbb_oauth_tokens        |
| phpbb_poll_options        |
| phpbb_poll_votes          |
| phpbb_posts               |
| phpbb_privmsgs            |
| phpbb_privmsgs_folder     |
| phpbb_privmsgs_rules      |
| phpbb_privmsgs_to         |
| phpbb_profile_fields      |
| phpbb_profile_fields_data |
| phpbb_profile_fields_lang |
| phpbb_profile_lang        |
| phpbb_ranks               |
| phpbb_reports             |
| phpbb_reports_reasons     |
| phpbb_search_results      |
| phpbb_search_wordlist     |
| phpbb_search_wordmatch    |
| phpbb_sessions            |
| phpbb_sessions_keys       |
| phpbb_sitelist            |
| phpbb_smilies             |
| phpbb_styles              |
| phpbb_teampage            |
| phpbb_topics              |
| phpbb_topics_posted       |
| phpbb_topics_track        |
| phpbb_topics_watch        |
| phpbb_user_group          |
| phpbb_user_notifications  |
| phpbb_users               |
| phpbb_warnings            |
| phpbb_words               |
| phpbb_zebra               |
| transactions              |
+---------------------------+
71 rows in set (0.00 sec)


rebuilding manual fails:

mysql&gt; select * from transactions;
ERROR 1146 (42S02): Table 'nyc_primary.transactions' doesn't exist
mysql&gt; CREATE TABLE accounting (
    -&gt;  id INT NOT NULL AUTO_INCREMENT PRIMARY KEY,
    -&gt;  trans_date TIMESTAMP,
    -&gt;  paid_current BOOL NOT NULL DEFAULT '0',
    -&gt;  active BOOL NOT NULL DEFAULT '0',
    -&gt;  cust_id int(10)
    -&gt; );
ERROR 1146 (42S02): Table 'nyc_primary.accounting' doesn't exist


The database exist:

mysql&gt; show databases;
+--------------------+
| Database           |
+--------------------+
| information_schema |
| mysql              |
| nyc_primary        |
| performance_schema |
| test               |
+--------------------+
5 rows in set (0.00 sec)



mysql&gt; desc transactions;
ERROR 1146 (42S02): Table 'nyc_primary.transactions' doesn't exist


How do I recover my missing data/tables?
I cannot even manually add the table structure:
You cannot move an InnoDB table in that manner.  The problem is that there is info in ibdata1, even if the table has its own "tablespace" (.ibd).

With 5.6, and if you created the table as "file per table", you can use "transportable tablespaces".  See online docs for details.