When enabling encryption on an ownCloud 8 installation and the user already has files in account, those files will be encrypted on the first login. A message will display saying “Initial encryption started. This can take a while…. Please wait.” If, for some reason the account gets stuck in this mode, it is because the migration_status value for the users account has been set to -1, instead of 1. When all the files have been encrypted, this value is set to 1. When set to 0, the initial encryption runs. To update this value, log into mysql and perform the following steps:
#mysql -u root -p use owncloud SELECT * FROM oc_preferences WHERE configkey="migration_status";
(the command just entered will show the migration_status value for all accounts)
UPDATE oc_preferences SET configvalue="0" WHERE configkey="migration_status" and userid="accountname";
(this command updates the bit to 0 for a specific account)
Now, log into account, and encryption process should continue / finish.
More useful and relevant information can be found via these links: