The auto action, which is what is encrypting the field, in my below reply should only execute if the fields value was changed.
www.joomlapolis.com/forum/developer-members-support/243927-crypt-custom-field-content?start=0#324714
It does this via the conditions. Are you using this auto action to encrypt the field or are you doing so with something else?
The best way to deal with this though really is a custom fieldtype plugin that stores it as encrypted and handles whatever checks you need. You can use any of our fieldtype plugins as examples for making such a plugin.