Issue that I have can be observed on any grid with checkbox selection and filtering enabled at the same time (I edit this demo https://demos.telerik.com/kendo-ui/grid/checkbox-selection by adding filtering an already I can see my problem).
I have a grid with 10 records with checkbox selection, filtering and "persistSelection" option enabled. I select a single record with a checkbox. I use filtering and only 5 records remain visible, selected record is not visible (didn't match the filter). When I clear the filter my selected record remains checked. If I do the same but filtering causes all records to disappear then after clearing the filter my selected record is no longer checked. So we can see that selection persistence works differently depending on results of filtering. That is confusing and looks like a bug.