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When working on the first input (file2), NR == FNR, it collects field 2's values into an array indexed by field 1.
When working on the second, it checks if field 3 begins with sign, and replaces...

Try
awk -F, 'NR==FNR {T[$1]=$2; next} $3 ~ /^sign/ {$3=T[$1]} 1' OFS=, file2 file1
empname,place,empdep
aaaa ,city1,001
bbbb,city2,002
dddd,city1,005
ffff,city5,007
hhhh,city7,009