Or did you by "check" actually mean that you need to reverse all "downloads" to "deletes"?
For that, select (all) items and click "Revert" button.

Or actually, if you need to do it always for all items, it probably means that you are using a wrong synchronization direction. If WinSCP wants to download all remote orphan files, then you have selected "Local" direction. If you instead want to delete all remote orphan files, you should have selected "Remote" direction. See
https://winscp.net/eng/docs/task_synchronize_full#direction
https://winscp.net/eng/docs/ui_synchronize

Select all the items that you want to (un)check and click (Un)Check.
See https://winscp.net/eng/docs/ui_synchronize_checklist#selecting_actions

Please make mass delete button for synchronization checklist, because I need to check every row for this operation