I personally don't put anything in my spray gun that I don't plan on having out of it within an hour or two. Perhaps I should mention that I typically use acrylic/enamel as that is what I'm more comfortable with through usage, and I can easily blend in repaired areas.
Have you considered using a touch up gun or an air brush for the smaller coverage areas? I have both and both do a surprisingly good job. Each is ideal for smaller quantity use, especially the air brush. Often I have glass jar containers of paint that I have used out of. They store well if I exhale into the container before closing it. Most paint type won't even skin over it this is done, a trick I leaned a couple of decades ago.
