I have 2 codeigniter installs running on the same server.
the first app is :
localhost/aa/index.php
second app is :
localhost/aa/invoice/index.php
If I may .... I have noted that those design problems which are not practical and goes against the normal convention shall provided a basis for long and deep rooted problems.... You should ask your self it is really necessary / advisable to share session data between 2 different version of a framework when we know they are 2 different version for the reason that they do things differently... I can only say that no matter what you do.. this design flaw shall make your architecture fragile and sooner or later you will have to dump it.
Plz let me know if later you find out otherwise..