As mentioned from @kthorngren, there is no build in way of tracking, if or how much custom searches are active.
If you are sure, that there is only one custom search is active a
$.fn.dataTableExt.afnFiltering.pop();
will work - there is big BUT:
$.fn.dataTable.ext.search
is an array which contains the search settings for custom search and for searchPanes.
An erasing of this array with $.fn.dataTable.ext.search = [];
or two pop()'s, allthough there is only one custom search is active --> will brake searchPanes.
e.g. if you have three panes active, this would mean:
$.fn.dataTable.ext.search[0] -> SearchPane Col1
$.fn.dataTable.ext.search[1] -> SearchPane Col2
$.fn.dataTable.ext.search[2] -> SearchPane Col3
$.fn.dataTable.ext.search[3] -> Custom Search -> safe to delete
$.fn.dataTable.ext.search[4] -> Custom Search -> safe to delete
Following code does the job in my case:
let lenOfSearchPanes = dt.settings()[0]._searchPanes.c.columns.length;
let lenOfSearchArr = $.fn.dataTable.ext.search.length;
let diff = lenOfSearchArr - lenOfSearchPanes
if (diff > 0) {
$.fn.dataTable.ext.search = $.fn.dataTable.ext.search.slice(0, -diff);
}