Hello the_terrible,
This is a core concept to Spine, what you do in your setup pose will influence everything in animate mode.
If you move a bone in setup mode, it will be moved accordingly in animate mode.
If you decide to change the color of the hair, it will be reflected in animate mode.
Animate mode is not absolute, but it will change relatively to the way you set up your skeleton in setup mode.

This can be a great advantage, expecially if you decide to add things on the go, but also dangerous if you're moving bones you didn't actually wish to change in all the animations.

Your playground to test poses should ideally be a blank animation. Not the setup pose.
If you add a mesh, you should later put all the bones back in the way they used so be.

So, maybe you messed up a little, how do you get everything back in place?

1. open the Spine settings (or press F12 if on windows)
2. navigate the menu until you find the backup folder
3. open the backup folder, find a file with a date before you messed up things
4. copy the file into your project folder so you won't see the missing images
5. maybe check that it is actually the file you wanted
6. open your project file
7. import project>import your backup file, select skeleton and not animations
8. now you have two skeletons. Spot the differences. If you find a bone moved around:
9. select the correct bone from the backup skeleton (it's easier to select if you deactivate your original bone) make sure to have world coordinates, press ctrl+c
10. reactivate the original skeleton and deactivate the other, select the corresponding bone
11. press ctrl+v and the bone will get back in place

you can select multiple bones at the same time, but they need to have the same names and structure, also, if there are IKs involved you need to select those too or the skeleton will do crazy things on paste.

Good luck and hope this helped!