So I do following actions on encrypted InnoDB :
[mysqld]
plugin_load=file_key_management.so
file_key_management_encryption_algorithm=aes_cbc
file_key_management_filename=/sec/keys.enc
file_key_management_filekey=secret
innodb-buffer-pool-size=128M
innodb-encrypt-log=ON
innodb-encryption-rotate-key-age=2
innodb-encryption-threads=4
innodb-tablespaces-encryption
innodb-encrypt-tables=FORCE

root@c480fbb475db:/test# mysql <<EOL
create database d1;
use d1;
create table t(a varchar(5)) encrypted=yes encryption_key_id=1;
EOL
root@c480fbb475db:/test# cp /dt/d1/t.ibd /t.ibd
root@c480fbb475db:/test# mysql d1 <<EOL
> drop table t;
> create table t(a varchar(5)) encrypted=yes encryption_key_id=1;
> alter table t discard tablespace;
> EOL
root@c480fbb475db:/test# cp /t.ibd /dt/d1/
root@c480fbb475db:/test# mysql -e "alter table d1.t import tablespace;"
ERROR 1296 (HY000) at line 1: Got error 39 'Data structure corruption' from ./d1/t.ibd

If I don't drop the table inbetween - it works.
Attached mtr test case shows the same error:

ALTER TABLE t1 IMPORT TABLESPACE;
encryption.innodb-discard-import-adv 'cbc,innodb_plugin' [ fail ]
Test ended at 2016-12-23 11:46:15

CURRENT_TEST: encryption.innodb-discard-import-adv
mysqltest: At line 134: query 'ALTER TABLE t1 IMPORT TABLESPACE' failed: 1296: Got error 39 'Data structure corruption' from ./test/t1.ibd