Reproducible in the Columns demo: https://demos.telerik.com/kendo-ui/gantt/columns
The parent's percent complete is also set to 100%. This is incorrect, since the other children of parent are not removed from the dataSource, they are just visually filtered. The problem becomes more evident, if the filter is cleared. Then the parent keeps its 100% value, even though it contains child tasks with percentComplete less than 100%.
The parent task percent complete should be consistent to the behavior without filtering applied. Using the same example, this means: on updating "Market" to 100%, Research should change its percentComplete to 49%, taking into account all of its children percentComplete values.