Unfortunately, by calling performBatchUpdates, the layout automatically animates all items itself. Even until now, there's no way to explicitly tell which items to animate and which not to.

However, I came up with a resolution which is kind of an anti-pattern.

For your header class, override these methods:

       -(void)setBounds:(CGRect)bounds
        {
            [CATransaction begin];
            [CATransaction setDisableActions:self.shouldDisableAnimations];
            [super setBounds:bounds];
            [CATransaction commit];
        }
    
        //-(void)setCenter:(CGPoint)center
    
    
        - (void)setCenter:(CGPoint)center
        {
            [CATransaction begin];
            [CATransaction setDisableActions:self.shouldDisableAnimations];
            [super setCenter:center];
            [CATransaction commit];
        }

Now if shouldDisableAnimations is true, the collectionView's automatic animations won't be applied to our header.

However, disabling the animations for the header may cause other glitches (e.g. when you scroll down a lot, and then remove all the cells. the header will jump to top instantly and the collectionView will scroll to top with animation resulting in a glitch!)

To handle this we need to set shouldDisableAnimations for the header in the correct time which is when prepareForCollectionViewUpdates gets called. Unfortunately, we cannot do this through the header's attribute since the attributes are applied to the header after animation gets finished. So we need to make direct access to the header's instance directly from within prepareForCollectionViewUpdates method. (there are several ways to do this. I did this by keeping a weak reference of the header on a class property of itself)

-(void)prepareForCollectionViewUpdates:(NSArray<UICollectionViewUpdateItem *> *)updateItems
{
    // Keep track of insert and delete index paths
    [super prepareForCollectionViewUpdates:updateItems];
    
    [self.indexPaths2Delete removeAllObjects];
    [self.indexPaths2Insert removeAllObjects];
    
    for (UICollectionViewUpdateItem *update in updateItems)
    {
        if (update.updateAction == UICollectionUpdateActionDelete)
        {
            [self.indexPaths2Delete addObject:update.indexPathBeforeUpdate];
        }
        else if (update.updateAction == UICollectionUpdateActionInsert)
        {
            [self.indexPaths2Insert addObject:update.indexPathAfterUpdate];
        }
    }

    if (self.indexPaths2Insert.count > 0 || self.indexPaths2Delete.count > 0)
    {
        HomeHeaderView.liveInstance.shouldDisableAnimations = false; //since it may cause scrolling, we should enable the animations
    }
    else
        HomeHeaderView.liveInstance.shouldDisableAnimations = true; //there's nothing added or deleted, so keep the header sticked.
}

The above solution I provided earlier seems not to work on iOS 13.

During performBatchUpdates, UICollectionView doesn't apply layoutAttributes for elements. The only way to fix this is to make set the frame (or any other parameters) on the header explicitly from within prepare() method of the layout. Because there's an ongoing animation being performed, UICollectionView won't layout during the animation.

I think Apple has to add a feature to explicitly mark which elements participate in the animation and which not. This can be done through the layoutAttributes of elements or a separate method in UICollectionViewLayout.

Accessing the element instances from layout is a no-no! But there's no other workarounds at the moment.

I was also having the same problem, but the work around I have done is reload the collectionView(the sticky header didn't disappears) it self instead of insert.