I'm tired. If you haven't figured it out by now...
You mean there are two identical files listed in the include list or with the first POP list having "#" all over themselves and the other list without "#"? I don't have Victoria so can't check but I remember it was the latter.
Because "GC file" and "POP folder" are quite vague descriptions, you might have meant the POP files themselves and not something you found while editing 1836.eug. So...
Open the 1836.eug and scroll to the "include" listing and search the names of the POP files. Then you know which ones the game uses. Or you can just open the 1836 directory and list the stuff by date and delete the oldest csv files or list by name and delete all which doesn't start with numbers while avoiding deleting inc's in both cases. Not sure if that method works.
From what I recall there were only one set of POP files per scenario folder in early versions of Victoria, but with some patch they released new POP files (maybe because they are atleast 4328975426418907158438247189347892641786573101893718926358976596540419418093471890651086510265873164018767631259059012375869345096176541805671085189743289754264189071584382471893478926417865731018937189263589765965404194180934718906510865102658731640187676312590590123758693450961765418056710851897432897542641890715843824718934789264178657310189371892635897659654041941809347189065108651026587316401876763125905901237586934509617654180567108518974328975426418907158438247189347892641786573101893718926358976596540419418093471890651086510265873164018767631259059012375869345096176541805671085189743289754264189071584382471893478926417865731018937189263589765965404194180934718906510865102658731640187676312590590123758693450961765418056710851897432897542641890715843824718934789264178657310189371892635897659654041941809347189065108651026587316401876763125905901237586934509617654180567108518974328975426418907158438247189347892641786573101893718926358976596540419418093471890651086510265873164018767631259059012375869345096176541805671085189743289754264189071584382471893478926417865731018937189263589765965404194180934718906510865102658731640187676312590590123758693450961765418056710851897432897542641890715843824718934789264178657310189371892635897659654041941809347189065108651026587316401876763125905901237586934509617654180567108518974328975426418907158438247189347892641786573101893718926358976596540419418093471890651086510265873164018767631259059012375869345096176541805671085189743289754264189071584382471893478926417865731018937189263589765965404194180934718906510865102658731640187676312590590123758693450961765418056710851897432897542641890715843824718934789264178657310189371892635897659654041941809347189065108651026587316401876763125905901237586934509617654180567108518974328975426418907158438247189347892641786573101893718926358976596540419418093471890651086510265873164018767631259059012375869345096176541805671085189743289754264189071584382471893478926417865731018937189263589765965404194180934718906510865102658731640187676312590590123758693450961765418056710851897432897542641890715843824718934789264178657310189371892635897659654041941809347189065108651026587316401876763125905901237586934509617654180567108518974328975426418907158438247189347892641786573101893718926358976596540419418093471890651086510265873164018767631259059012375869345096176541805671085189743289754264189071584382471893478926417865731018937189263589765965404194180934718906510865102658731640187676312590590123758693450961765418056710851897432897542641890715843824718934789264178657310189371892635897659654041941809347189065108651026587316401876763125905901237586934509617654180567108518974328975426418907158438247189347892641786573101893718926358976596540419418093471890651086510265873164018767631259059012375869345096176541805671085189743289754264189071584382471893478926417865731018937189263589765965404194180934718906510865102658731640187676312590590123758693450961765418056710851897 times easier to manage). The patch doesn't delete the old ones. So the stuff with "#" front of themselves are useless and don't do anything.
You can add, duplicate, delete, in short do whatever allowed to the POP files but you have to edit the include listing in the 1836.eug for them to take effect.
If you add, duplicate, delete or in short do whatever allowed to the POPs inside the POP files you don't have to do anything additional hocus pocus because the 1836.eug already knows it has to read that file you edited.
For the other question read
http://forum.paradoxplaza.com/forum/showthread.php?t=133707 . It has been answered at least one time, but more likely at least two dozen times.