Спросите пользователя перед отправкой формы

Вы можете попробовать удалить onsubmit и использовать кнопку для открытия модального окна, а затем вызывать exportExcel при нажатии кнопки «Да»:

<form action='@Url.Action("ExportExcel", "Records")' method = "post" target = "_blank" id = "myForm">
    <input type = "hidden" name = "filteredRecordsIds" id = "filteredRecordsIds" value = "" />
    <input id = "btnExportExcel" type = "button" value = "submit" data-toggle = "modal" data-target = "#exampleModalLong"/>
</form>

<!-- Modal -->
<div class = "modal fade" id = "exampleModalLong" tabindex = "-1" role = "dialog" aria-labelledby = "exampleModalLongTitle" aria-hidden = "true">
    <div class = "modal-dialog" role = "document">
        <div class = "modal-content">
            <div class = "modal-header">
                <h5 class = "modal-title" id = "exampleModalLongTitle">Modal title</h5>
                <button type = "button" class = "close" data-dismiss = "modal" aria-label = "Close">
                    <span aria-hidden = "true">&times;</span>
                </button>
            </div>
            <div class = "modal-body">
                Would you like to export with calculations?
            </div>
            <div class = "modal-footer">
                <button type = "button" class = "btn btn-primary" onclick = "exportExcel()">Yes</button>
                <button type = "button" class = "btn btn-secondary" data-dismiss = "modal">No</button>
            </div>
        </div>
    </div>
</div>

js (отправьте форму в exportExcel):

function exportExcel() {
            $('#filteredRecordsIds').val(filteredRecords.map(function (record) { return record.Id }));
            $("#myForm").submit();
        }