Okay, so, there's a couple things in play here you need to be aware of. Keep in mind that some of this is slightly speculative.
First, it is only in the dub that Alphonse states it to be the "one and only" truth. The original commentary states,
"When we were young, we believed that to be the truth of the world."
Second, though, I think there is an important reason that Alphonse brings this up. Starting at episode 43, the pre-OP commentary changes to the following:
He who obtains [the Philosopher's Stone] is exempt from the rule of Equivalent Exchange and does not have to sacrifice anything to obtain something.
(Note: This statement is somewhat wrong: During this unusual exchange, there is still something lost, but it's not apparent to whomever it is doing the transmutation.)
In their adventure, Ed and Al basically learned that human lives are given an alchemical value; since they both believe human life to be invaluable, this shakes the foundation of the principle of Equivalent Exchange that they grew up learning.
This seems to be the only reason that Alphonse used the past tense with "believed"; the Philosopher's Stone shattered what they believed Equivalent Exchange truly meant. To him, Equivalent Exchange can no longer be the "one and only" truth.
This idea also holds true in Brotherhood. The Philosopher's Stone is essentially identical, and the brothers learn the same terrible details of it.