Restore InnoDB from .frm files
Two potential workarounds:

Simulate the internal InnoDB table counter. That is, create work tables (with innodb_file_per_table enabled) until you have the internal pointer of table id equal to (1 – id_of_ibd_table_you_need_to_restore).
Manually hex edit the .ibd file, changing the table id.

See Recovering an InnoDB table from only an .ibd file for the full explanation and the detailed steps involved.