While making a revised baseline using the current update you may get a variance, i.e. Schedule Percent Complete and Performance Percent Complete may not be the same even when the baseline is a copy of the current update and no changes have been made.
You need to adjust the settings in P6 to resolve this issue.
Go to Admin preferences > earned value > earned value calculation > “when calculating earned value from a baseline use” > Click “Budgeted value with current dates”.
This will set all planned values equal to actual values. You may still face some problems in cases where some activities are still in progress. I suggest you take additional steps and break these activities in two parts; completed, and remaining. Then you won’t have any problem at all.