innodb table does not exist
This sounds like all your .ibd file have been detached. Why ?

Please look at the InnoDB Architecture from Percona CTO Vadim Tkachenko



ibdata1 has an internal data dictionary that registers every .ibd by a unique tablespace_id. Somewhere along the line, all the tables in the trouble database have become detach from the data dictionary.

I wrote about this years ago


Apr 23, 2012 : How can extract the table schema from just the .frm file?
Dec 21, 2011 : Table compression in InnoDB?


To rightfully give credit where credit is due, I learned about this concept of detached .ibd files and trying to connect them back to the data dictionary from a blogpost written by Chris Calendar back in Feb 2009. I once helped client recover 30 tables with the information from his post (See my post ERROR Cannot find or open table? on what I did to help that client). Please read his biog and then my posts on what you need to try.

As for the why the table would be come detached, here is an example


Your datadir is /var/lib/mysql
Your have a database called mydb
You have a table called mytable


If you create an InnoDB table called mytable in the mydb database


You get two files


/var/lib/mysql/mydb/mytable.frm
/var/lib/mysql/mydb/mytable.ibd

.ibd file would be assigned a tablespace_id.


If you drop that table and create it again, the table would have a different tablespace_id.

Now, picture this:


You make a backup of the database folder /var/lib/mysql/mydb with the tablespace_id of 27 on that one table
You drop the table and create it (TRUNCATE TABLE internally does the same thing), ending up with tablespace_id of 28
You restore the backup of the database folder /var/lib/mysql/mydb with the tablespace_id of 27 on that one table


This causes the detachment because table mydb.mytable has the old tablespace_id of 27 while the data dictionary within ibdata1 has 28.

Since you said you didn't move or copy anything, then you may have too many InnoDB tables. Each InnoDB table needs two file handles to be opened and accessed. 

I hope I have given your the information you need to help you recover your database.