When Godot saves scenes, it saves parameters that were changed. For example, if you have a
Sprite with a scale of 1, the scale will not be recorded as it is the default value. However, if it has a scale of 2, then the scene will be saved with the scale because it's not the default value.
This size increase is insignificant and shouldn't make any difference in file size.
I strongly recommended that you make a copy, put back the old textures and return the scale then exporting again. You may have changed something in your project so check again.