The first expression is a continued fraction, the second isn't. A continued fraction is the limit of
$$ a_0, a_0 + \frac{1}{a_1}, a_0 + \frac{1}{a_1 + \frac{1}{a_2}} \ldots $$
for a **fixed** sequence of natural numbers $a_0, a_1, a_2 \ldots$

The second expression is the limit of fractions which look similar to these fractions, but which don't correspond to one well-defined sequence of naturals. The first lot of dots (between the equals signs) are ok, they just mean 'take the limit of this process'. This limit exists and is equal to 2, as you correctly deduce. The dots at the bottom of the final expression falsely suggest that the limit is a continued fraction, with coefficients given by the obvious sequence (eg $2, 2, 2, 2, \ldots$ implies the sequence consisting of only twos).

As @Did points out very elegantly, the same rules apply to infinite sums, and seem more obvious there - an infinite sum is not the same as the limit of an infinite sequence of sums, each with more terms in it than the one before. The common terms have to agree for any two sums.

I think this misunderstanding arises because sometime in iteration and limits we have the sense that the initial terms don't really matter, and sometimes this is the case. The first few terms of a sequence don't affect the limit, or the limit of the average, etc.

You are taking two different starting terms and iteratively applying a transformation to them. As you point out, this transformation doesn't actually change the number. This fact means though, that the starting value never becomes unimportant, and the final terms of each expression in your sequence similarly never become unimportant.