First, it means "This asteroid was seen only once through a telescope..."
I agree the use of negative form seems odd, and there are a few like that in French.
Basically, there are two ways to say this :
- Cet astéroïde n' a été aperçu qu' une fois.
- Cet astéroïde a été aperçu une fois.
They mean almost the same thing, though the latter does not necessarily mean the asteroid was not spotted again later on. But that's your starting sentence, to which the added words forming the first sentence exclude that possibility.
If I were to give you a plausible explanation, I would say that the first one is presumably a contraction of
Cet astéroïde n' a pas été aperçu plus qu' une fois.
(The correct way to say this would be "plus d'une fois" instead of "plus qu'une fois" but if you don't already know that I would stick with the slightly incorrect one for this topic, which most French people wouldn't even notice)
Here, negative form makes sense because we are saying that it wasn't seen more than once.
Maybe an English phrase offering a good one-to-one word correspondence with your sentence would be "This asteroid was not seen but once through a telescope..."
However I wouldn't assume "que" and "but" to have similar meanings in general.
Actually as Simon Déchamps suggested in a comment, a better French translation of this "but" would be e.g. "sauf", so I might also say that "que" has a "sauf" meaning. This explains the structure pretty well I must say. In this interpretation, your phrase is actually a negative phrase, implicitly.
Sometimes you have to twist things a little to spot the similarities, especially since French and English have very different grammar.