Hi Bert,
I've made a note to look into this, in the mean time, you can add this to your user.config file then you will see a new button on the Store Manager page for Rebuild Reports. It is hidden because I don't think it should be done frequently and may be more problematic after there are thousands of orders. Ultimately I think everything should keep itself synced, but this feature does exist and I think it will correct your reports.
<add key="ShowRebuildReportsButton" value="true" />
Hope it helps,
Joe