If you are experiencing any issue with the atlas season branches where some nodes that offers multiple options shows multiple check icon, then you are experiencing a inconsistent progress.

This issue occurs mostly to players that somehow was able to claim rewards beyond what they can afford. To fix this, please go to another branch and claim any nodes that isn't causing a sync error. After claiming, exit atlas and enter again. Going back to the branch shouldn't cause any issue.

If you notice that some progress were lost from the atlas season branch, those are the claims that did not cost you any badges nor provided you any items despite showing a check icon. Rest assured that you did not lose anything during the whole issue based on multiple cases that was handled by Support.