moving binary database folder is causing issues with innodb tables
You cannot copy a database folder that has InnoDB tables because InnoDB storage engine maintains a symbiotic relationship between the InnoDB tables' physical files (frm and .ibd) and the data dictionary.



The data dictionary is inside the system tablespace file known as ibdata1.

You cannot copy a data folder and expect it to be independent of ibdata1. 

SHOW TABLES; works because it only scans for .frm files and does not access metadata.

You could do one of two things


mysqldump the database and load the mysqldump into the target server
Run FLUSH TABLES;, disconnect the .ibd files from ibdata1 before copying to the other server. Then, reattach the .ibd files on the target server


Recover MySQL database from data folder without ibdata1 from ibd files
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GIVE IT A TRY !!!