Entity Framework Core: Global query filter not filtering correctly after data change

We implemented a soft deletion pattern with Entity Framework Core, very similar to this solution, but with a nullable column "DeleteDate" instead of an IsDeleted flag. If the date is filled, the row is considered deleted and filtered out:

modelBuilder.Entity<TEntity>().HasQueryFilter(e => !EF.Property<DateTime?>(e, "SysDeletedOn").HasValue);

The following code bit would update one item while doing so, delete one of its child elements, but in the returned item, the deleted child would still be contained. Only a new query of all items would filter the children collection correctly.

public async Task<Item> UpdateItemAsync(ItemDto itemDto)
{
    var itemEntity = await _context.Items.SingleOrDefaultAsync(i => i.Id == itemDto.Id);

    if(itemEntity != null)
    {
        return;
    }

    // Update item's properties here
    // ...

    foreach (var child in itemDto.Children)
    {
        // Update child here
        // ...
    }

    foreach (var child in itemDto.RemovedChildren)
    {
        var childEntity = await itemEntity.SingleOrDefaultAsync(i => i.Id == child.Id);
        _context.Remove(childEntity);
    }

    await _context.SaveChangesAsync();

    // Read and return updated item
    return await _context.Items.SingleOrDefaultAsync(i => i.Id == itemDto.Id);
}

The question is now: How can I get the correct list in this method after this change (deletion) has been made? Do I have to clear the cache somehow between SaveChangesAsync and reading the context again?

The regular updates (property values) of the item are returned correctly. Also, it works when I query the items with .AsNoTracking() which also turns off caching, obviously.