Thanks for the bug report, I can confirm this is happening.

I encountered a similar bug where org-agenda-prepare-buffers was causing 
the same issue when the file hadn't been saved to disk, and I agree that 
the solution looks good. I've formatted this into a patch and attached 
it. Might be worth considering too if this is happening anywhere else 
too, since this is the second time it has come up.

On 5/11/21 6:07 AM, mail@kisaragi-hiu.com wrote:
> * Reproduction
>
> 1. emacs -Q
> 2. C-x C-f /tmp/new.org RET
> 3. Type anything
> 4. Type C-u C-c # (C-u org-update-statistics-cookies) to try to update all statistics cookies in the buffer
> 5. Notice the "Non-existent agenda file /tmp/new.org." error.
>
> This doesn't happen if the file already exists.
>
> I first saw this reported in this reddit thread: https://www.reddit.com/r/orgmode/comments/n9g1yf/is_this_a_bug_with_orgupdatestatisticcookies/ (u/flyin1501 is me)
>
> * Expectation
>
> All statistics cookies in the buffer are updated no matter if the buffer's associated file is already created or not.
>
> * Why this is happening
>
> - `org-update-statistics-cookies` (C-c #) uses `org-map-entries` to update all cookies.
> - `org-map-entries` uses `org-agenda-prepare-buffers` to prepare the file when SCOPE is nil. Excerpt:
>
>          (if (not scope)
>              (progn
>                (org-agenda-prepare-buffers
>                 (and buffer-file-name (list buffer-file-name)))
>                (setq res
>                      (org-scan-tags
>                       func matcher org--matcher-tags-todo-only start-level)))
>
> - This function complains if the file does not exist, causing the error.
>
> * Solution (IMO)
>
> `org-map-entries` is quite complex because of its matching and scoping features; `org-update-statistics-cookies` only updates the current buffer and should use `org-map-region` instead. IMO it should go from
>
>      (if all
>          (progn
>            (org-update-checkbox-count 'all)
>            (org-map-entries 'org-update-parent-todo-statistics))
>
> to:
>
>      (if all
>          (progn
>            (org-update-checkbox-count 'all)
>            (org-map-region 'org-update-parent-todo-statistics (point-min) (point-max)))
>