% complete can either be manually calculated or indirectly calculated based on other fields such as Actual/Remaining Effort. Normally the % complete rollup is also weighted based on how much work each task requires. However, if you have an empty milestone in your project plan, that will change the weighting and is a primary cause of inconsistencies with % completion. If you would like us to do a specific investigation, we would recommend submitting a ticket along with the mpp file and an access link.
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