As the title says, if there are any items in the Compactor's input slot when you select a recipe with JEI, those items will be deleted. This is version 2.0.6.

Steps:

• Place items in Compactor input slot. I used a stack of Silicon Dioxide.
• Choose recipe from JEI. I chose Andesite.

As you can see in the attached GIF, the stack already in the Compactor is deleted and a single item from my inventory is input.

Hello. This was fixed in 2.0.8a. I completely rewrote the transfer handlers to prevent them from deleting items. I will ask Cryptic who makes the Encrypted modpack to update soon.