So it wasn't that the second perform find step redid the first. Rather, the second find didn't execute at all, if I understood correctly. I solved this by doing:
Enter Find Mode
Set Field[Table::ID; $Var2]
If[Get(FoundCount) = 0]
Show Costum Dialog["None found!"]
(In reality I want to execute a script for If[Get(FoundCount) > 0] , which I don't need to do if the variable is empty as I know there are no empty ID's.)
Just change the Set Variable to Set Variable [$Var2;Value:"="] as stated above. The equal sign (=) by itself in a find, finds empty records.