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Yes that is correct, #3 uses exact strings, so it correctly identifies the right field, and the sub() in itself isn't the problem either, since iteration occurs over the fields and not over the key...

Hi, try:
awk '
NR==FNR {
A[$1]=$2
next
}
{
for(i=1; i<=NF; i++)
if($i in A)
sub($i,A[$i])
print
}
' FS="=" file2 FS='[(/,]' file1