$ cat in.txt 
a b "x1	x2"
c d "x2"
e f "x3	x4	x5"
$ perl -ple 's/(?<=")([^"]*)(?=")/(my$x=$1)=~s#\t#,#g;$x/ge' in.txt 
a b "x1,x2"
c d "x2"
e f "x3,x4,x5"
$ perl -ple 's/(?<=")([^"]*)(?=")/$1=~s#\t#,#gr/ge' in.txt 
a b "x1,x2"
c d "x2"
e f "x3,x4,x5"