When applying a redstone signal to the lower gantry shaft the item held by the deployer vanishes to never be seen again. This only happens if there is rotation on the gantry shaft when the redstone is applied.

Thanks for reporting this, the issue seems to now be fixed on the dev branch.

Here's a video for reference: https://www.youtube.com/watch?v=IVCcMguDWv0

Can confirm this as well saw with my own eyes and caused the amazing sheep shearing farm to break, this bug definitely needs to be looked at asap.