There are two ways to decrypt scripts with SQL Admin Tools Quick Compare, automatically via the menu setting and manually when viewing a script.
Enabling the menu item to compare encrypted scripts will slow down database comparisons but will automatically decrypt scripts before comparing them.
Any script that is displayed thorugh the right click menu or displayed by clicking on it will clearly indicate if it is encrypted.
Double clicking on any script that is listed as Encrypted will attempt to decrypt it.
Whether selecting the menu item or double clicking on the script to decrypt it, encrypted scripts can now be compared with unencrypted counterparts.
Please Note: Decrypting scripts requires Dedicated Administrator Connection (DAC). This ensures that only authorised personel can access encrypted scripts. This limmitation is clearly stated if a decrypt attempt fails.
Please see here for more details in relation to the limmitations of DAC as well as enabling DAC on SQLExpress or across a network.