Let's get a clearer picture of the situation.
You had this:
master
v
*---*
\
\
*---*---*---*---*---*---*
^ ^
X Y
You then merge X into master:
master
v
*---*-----------------*
\ /
\ /
*---*---*---*---*---*---*
^ ^
X Y
And now you want to merge Y into master.
This is entirely fine, and assuming, as you say, that no other changes have been made on master, there will not be any additional conflicts.
You will end up with this:
master
v
*---*-----------------*-----------*
\ / /
\ / /
*---*---*---*---*---*---*
^ ^
X Y
A similar situation would've arose if you had never made Y, merged X into master, but kept working on X, and finally merged X yet again into master, then you would just have this situation:
master
v
*---*-----------------*-----------*
\ / /
\ / /
*---*---*---*---*---*---*
^
X
Which is the same situation except for which branch names are involved.