while IFS=$'t' read -r line ; do
some code.. (to get the value of $some_var and $another_var)
echo "$line" | awk -v var1="$some_var" -v var2="$another_var" -F $'t' 'BEGIN {OFS = FS} { $1=$var1 } ; {if($2!="") $2=$var2 }; { print }' >> file.tsv
done < text.tsv

File content:
A    B         D
1         3    4

Intended output
H    I         D
6         3    4

Output I get:
               D
          3    4

while IFS=$'t' read -r line ; do
  some code.. (to get the value of $some_var and $another_var)
  echo "$line"
    | awk -v var1="$some_var" -v var2="$another_var" -F $'t'
         'BEGIN {OFS = FS}
          { $1=var1 }
          {if($2!="") $2=var2 }
          { print }' >> file.tsv
done < text.tsv