Do you have an official proof that they were broadcasted (not produced) as a 2nd season ?

The fact that there was a multiple months break between them doesn't necessary mean that it was a new season.

All the animation databases, Wikipedia and other sources I have found all mentioned the show broadcasted as two seasons: https://cartoondatabank.com/cartoons/secret-squirrel-1965/ https://reelrundown.com/animation/History-of-Hanna-Barbera-The-Atom-AntSecret-Squirrel-Show https://www.toonopedia.com/secsqurl.htm

As indicated, we need an official proof that they were broadcasted as "season 2" at the time of the original broadcast.

Official proof can be, for example, archived copy of TV schedules or newspapers from the time of the broadcast, explicitely indicating that this is a 2nd season.

Without this, we prefer having a single list of episodes.

What you are asking is quite impossible, I have found the TV guide for that date (https://archive.org/details/vintage-tv-guides/TV%20Guide%201966-09-10%20Northern%20CA/page/n43/mode/2up) and other newspaper TV schedule for that date and the information provided then was quite limited for the cartoons. There is not information about seasons or even episodes name. The fact that you prefer to have a single season doesn't mean that the information is correct, since the show was produced and has two seasons.

@blu-mim said:

since the show was produced and has two seasons.

We don't list the shows as they were produced, but as they were broadcasted.

Do you have prove that the show was broadcasted as a single season?

@blu-mim said:

Do you have prove that the show was broadcasted as a single season?

Without proof of a split, we list by default the shows as one single season.