Here is a solution for $N=9$ which can be extended to $N=11$:
As an example, the numbers picked might be {1,4,7,8} as indicated by red dots in the following diagram:
Then the assistant could
arrange the cards in the order 714 and then the magician could deduce that the missing number is 8.
OR the assistant could
arrange the cards in the order 874 and then the magician could deduce that the missing number is 1.
How does the magician decode the assistant’s card order:
The first number in the assistant’s ordering is the base number.
The second and third number tells the magician how far to advance clockwise from the base number to get the hidden number.
If the second number is less than the third number, advance one position. For example if the ordering is 714, the base number is 7 and since 1<4, the magician advances clockwise one position from 7 to get 8 (the hidden number).
If the second number is greater than the third number, advance two positions. For example if the ordering is 874, the base number is 8 and since 7>4, the magician advances clockwise two positions from 8 to get 1 (the hidden number).
How does the assistant determine the card order:
First, the assistant picks one of the audience’s chosen numbers (which will be the base number) such that if you advance one or two positions clockwise from the base number you get to another audience chosen number (which will be the hidden number).
Secondly, the assistant places the base number in the first position, sets aside the hidden number, and arranges the two remaining numbers in the second and third positions to indicate the number of positions to advance.
Will the assistant always be able to follow the above procedure no matter what numbers are chosen by the audience:
Yes!
Let the 4 audience chosen numbers be A,B,C,D such that if you start at A and proceed clockwise the next number will be B then C then D. To advance from A to B you go $P_1$ positions, from B to C $P_2$ positions, from C to D $P_3$ positions and lastly from D back to A $P_4$ positions.
$P_1+P_2+P_3+P_4=9$ (all away around the 9-gon)
At least one $P_n$ must be $\le 2$ because otherwise $P_1+P_2+P_3+P_4 \ge 12$
Therefore, using a $P_n$ value that is $\le 2$, the assistant can always pick a base number and then complete their procedure.
The above method will work even if the range of possible audience chosen numbers is expanded to 1,2,3,...11.