Should I disconnect the existing Facebook pixel after connecting AnyTrack?

Short answer: yes.

After connecting AnyTrack with Shopify and Facebook pixel, it will generate Purchases and other conversion events on your store. By turning on Facebook Conversion API,  AnyTrack will start to send data to the connected pixel back to Facebook.

In order to prevent event duplications, you will need to disable your current Shopify ad networks integrations.

Alternative options:

• Set up AnyTrack on separate pixel ids - In this way, AnyTrack will send the data to one pixel and the existing facebook-shopify connecting will send the data to another pixel. 
• Another option is to map the events from AnyTrack to different events in Facebook pixel.

In the next example, AnyTrack sends to Facebook pixel the purchases by "purchase AnyTrack" event, while in the facebook-Shopify connection the purchases are related to a different event, for example "purchase". In this case, the conversions from AnyTrack will be listed for one event and the conversions from facebook-Shopify connection will be listed for another event.