Yes, "but" can indeed be be a synonym for "except" in some cases, particularly in old-fashioned writing. However, that's not the case here.
Even ignoring the contextual information (that "slave" and "son" are usually contradictory), a sentence like:
*"You are no longer a slave, except a son."
or, more generally:
*"[X] is a [Y], except a [Z]."
is not even meaningful English: it appears to state that some specific subject (X) is something else (Y), but then excludes something (Z) from this statement, even though there's nothing to meaningfully exclude (since the preceding statement applies only to a single subject X, not to a group of subjects from which one could be excluded).
One thing that might potentially confuse you here is that the English pronoun "you" can be either singular or plural, and even the verb "are" doesn't help tell these possibilities apart. However, since what "you" are claimed to (formerly) be is "a slave", it is clear that "you" here must be singular: multiple people could be "slaves", but they cannot all be "a slave".
So a sentence like the following could be meaningful:
"You are no longer slaves, except John, who still is a slave. (Sorry, John.)"
and, in that sentence, the word "except" could, indeed, be replaced by "but". But the fact that "a slave" is singular in the original sentence rules out an interpretation like that, even if common sense and the surrounding text did not.