Comment 4 for bug 1444255

The possible workaround is to decrypt xtrabackup_checkpoints.xbcrypt prior taking backup as:

# xbcrypt -d -k 'VVTBwgM4UhwkTTV98fhuj+D1zyWoA89K' -a AES256 -i xtrabackup_checkpoints.xbcrypt
backup_type = full-backuped
from_lsn = 0
to_lsn = 2541071
last_lsn = 2541080
compact = 0
recover_binlog_info = 1

Or to store decrypted xtrabackup_checkpoints.xbcrypt:
# xbcrypt -d -k 'VVTBwgM4UhwkTTV98fhuj+D1zyWoA89K' -a AES256 -i xtrabackup_checkpoints.xbcrypt -o xtrabackup_checkpoints

[root@tokubackup 2017-01-20_13-12-43]# ls
backup-my.cnf.qp.xbcrypt dbtest ib_buffer_pool.qp.xbcrypt mysql qptest xtrabackup_checkpoints xtrabackup_info.qp.xbcrypt
ccc fff ibdata1.qp.xbcrypt performance_schema sys xtrabackup_checkpoints.xbcrypt xtrabackup_logfile.qp.xbcrypt

Then to run incremental backup:

/usr/bin/xtrabackup --defaults-file=/etc/my.cnf --user=root --password='Baku12345#' --target-dir=/home/backup_dir/inc/2017-01-20_13-30-15 --incremental-basedir=/home/backup_dir/full/2017-01-20_13-12-43 --backup --host=127.0.0.1 --port=3306 --compress=quicklz --compress-chunk-size=65536 --compress-threads=4 --encrypt=AES256 --encrypt-key='VVTBwgM4UhwkTTV98fhuj+D1zyWoA89K' --encrypt-threads=4 --encrypt-chunk-size=65536

0120 13:30:20 completed OK!

Thanks @Sveta for great advice.