The Philippine Statistics Authority (PSA) says not to worry!
In a facebook post, they said:
“Lumalabas ang status na NOT FOUND sa tracking site dahil maaaring ang iyong PhilID card ay idi-dispatch pa lamang sa Post Office. Hindi nito ibig sabihin na nawawala ang iyong PhilID card.”
PSA Facebook Post
We were right to assume that the “Not Found” status simply meant the PhilID may not have been dispatched yet by the PhilPost (Post Office).
We have to remember that the tracking service is by the PhilPost or the Philippine Government’s Official Postal Office. It does not have jurisdiction or authority over the manufacturing or processing of your PhilID (Philippine National ID). They simply deliver the PhilID to your homes/registered address.
Therefore it follows that with a “Not Found” status, your PhilID National ID card may in all truth and reality be intact and still processing, but just not yet dispatched for delivery and is not yet in the PhilPost system.
Here’s the PSA’s full post on the matter:

Bakit sobra tagal 1 year napo naghihintay dito sa compound namin nauna kmi nag pa register and yet kami paung wala hangga ngayon
same