if you run this command (please replace XXXX with you NC ID) you will probably see that updater finished step 9, what is deleting of an old NC installation:
cat /var/www/nextcloud/data/updater-XXXXXX/.step
If this is a case, please follow instructions from this post: Update to 13 fails - core/shipped.json is not available - #4 by gas85
There is even “one command” solution for this case: