Hello again.
Abaye holds that we don't say that a Mechitza can create an Issur.
However by a Chabura who is eating their Korban Pesach together we do say that a Mechitza between them invalidate their group.
Thank you very much.
The Rambam (Hilchos Korban Pesach 9:3) writes that when two Chaburos are eating in one house, each Chaburah must make a "Hekef." The Kesef Mishneh writes that it is possible that a "Hekef" does not mean that literally a Mechitzah is required, but rather the important thing is that the groups should not sit opposite each other because this would look as if they are one group.
According to this, we have an answer to your question. It is not the Mechitzah that invalidates one Chaburah, but rather what creates the Isur is that they sit in a way that looks as if they are not all in the same group, even if there is not actually a Mechitzah between them.
Kol Tuv,
Dovid Bloom
Here is a differrent answer to this question:
The Mechitzah you mention concerning the Chaburah is not considered a Mechitzah for an Isur but rather it is called a Mechitzah for a Mitzvah. When the Mechitzah was made between the two groups, this enabled each group to perform the Mitzvah on its own, so we do not consider this as a Mechitzah that created a prohibition but rather as a partition built with the purpose of performing a Mitzvah.
Dovid Bloom