Thank you for your follow up.
There is a scenario where the icon setting is "lost" in the aip file. I do not know exactly what that is yet. Going back and setting it again as you described addresses the issue.
I'm not sure if this is the case, but this might happened if the setup project was moved from his original location. The referenced icon path from disk is saved relatively (to the AIP project path) in the setup project. Thus, when moving the setup project if its referenced resources are not moved accordingly (relatively to the AIP) they won't be detected.
Also, there may be the case when the icon was moved (on disk) at different path since it was added in the setup project.
However, just try to find out a pattern if this issue occurs again.
All the best,
Daniel