# For example there are two files:
# fileA:
# 1    0
# 2    1
# 3    1
# 4    0
# fileB:
# 1    0
# 2    1
# 3    0
# 4    1

awk -v OFS='\t' 'NR=FNR{a[$1]=$2;next} NF {print $1,((a[$1]=$2)? $2:"0")}' fileA fileB
# 1    0
# 2    1
# 3    0
# 4    0