The ? rolls up, so if there is any ? in a sub item it will carry over to the milestone and project. If you are importing from MSP, you can either manually set the % at the milestone level or get rid of all the ? for the sub-items. If that does not work, you will have to open a case for deeper investigation.
As a side-note for the community, usually these ? are caused by tasks that should be completed based on the amount of time reported. The best practice for time tracking is to enter in both the time and the remaining effort (or % completion). This will get rid of the ?s in your projects.
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