Hi!
Can you share details from your 'Filter Array'? I think the problem is, your Filter Array is providing all 'Get items' outputs, and since you placed 'Update item' inside the 'Apply to each 2' you are overriding all SP list entries.
So the key is, which entries do you need to update (not all, right?), how to define this requirement in your 'Filter Array' and how to get rid of 'Apply to each 2'... I believe you can remove it by doing the folowing:
-Delete 'Apply to each 2' and its content
-Remove temporarily 'Filter array' output assigned to 'Apply to each' input, assign 'Get items' output instead
-Now, add 'Update item', configure its inputs
-Once 'Update item' inputs are configured, remove 'Get items' output assigned to 'Apply to each' input, assign 'Filter array' instead
Hope this makes sense