Deleted files for node are being included in view for services
You should use file_usage_delete to remove file usage records to nodes that files was having relations so you stop that problem for future deleting files on nodes.

And you still have to fix it for the existing nodes I suggest two ways

first : write a script to loop on file_usage records and check if the not currently used in the node (via node load and check fid exist) if so delete that record (if u have small number of rows in that table)

secod : Implement hook_views_pre_render  and do the same check.

the first is preferred however it may take long time but it will stop the problem reason