MatMartel ：

On export the project says it's missing images for certain attachments. They weren't being used for anything so I removed them to clean it up

If the error shows up, it means you probably only removed them from the folder, but not from the project. You need to delete these attachments from the Spine project as well to stop the warning from showing up.

MatMartel ：

and the scale of the character they were related to has doubled when it is brought in to the Spine Widget by the Dev.

This makes it sound like you have several characters in the same project? (I may have answered below)

MatMartel ：

If I leave the attachments in the project, and leave the error message, the character remains the same size.

Were the attachments meshes or simple attachments? I don't recall a project changing scale because of the attachments, unless something is going on with mesh textures being resized in the character perhaps and causing to need a bigger atlas? (wild guesses until I can see the project)

MatMartel ：

The Dev says the .atlas file is for some reason doubling the size, but not being a Dev myself I don't know why that would be happening.

You can check the packing settings when you export the json. if the scale is set to 2 instead of 1, then this is the reason why the scale doubles.
Texture Packing - Spine User Guide

Please check if deleting the attachments and checking the texture atlas size solves the problem, otherwise, if you wish I can give a look to the project if you send it to contact@esotericsoftware.com mentioning this topic, I will also need more details about the problematic attachments in question.