If you have a custom field that is of type checkbox, the intent was to allow the selection of more than one item. When using an automation to select one more item, all existing selected items will be removed. There is not a great way right now to evaluate which existing items are present so that you can re-select them in the automation either.

I propose that when selecting a checkbox item with automations, the existing selections should remain.

For example:

Pick ALL the colors you like:

[X] Red

[X] Green

[ ] Blue

If the automation adds Blue, it will remove Red and Green unless you re-select Red and Green at the same time.