Thanks a lot. I tried your code but it didn`t work.
It announced at Set Wb = Workbooks.Open Argument not optional.

As I`m a coding muggle and I didn`t want to spend time fixing the part which in the original code worked I went back to that code.
In the end the aim changed a bit (not deleting the value in the adjacent cell but replacing the zero by E20). Then we found problem with the target sheets being called differently in each file. Anyway this, even though it might not be nice or strictly correct, works:

Sub MonitoringCisteni()

Dim Wb As Excel.Workbook
Dim fso As Scripting.FileSystemObject
Dim f As Scripting.File
Dim AdresaSlozky As String

Dim F1 As Range
Dim F2 As String

AdresaSlozky = InputBox("Zadejte plnou adresu složky ve formátu S:\3A14119_plavebni_stupen_decin_experimentalni_vyhony\Podklady\Prijate\3A12042_87_12042_vyhonydvz")

Application.ScreenUpdating = False 
Set fso = New Scripting.FileSystemObject
    For Each f In fso.GetFolder(AdresaSlozky).Files
    Set Wb = Workbooks.Open(f)
    
    With Wb
        With ActiveSheet.Range("B2", "B5000")
        Set F1 = .Find(What:=0, LookIn:=xlValues, LookAt:=xlWhole, searchorder:=xlByRows, searchdirection:=xlNext)
        
        If Not F1 Is Nothing Then
            Do While Not F1 Is Nothing
                F1 = "E20"
                 Set F1 = .FindNext(F1)
            Loop
        End If
        End With
    End With
      
    Wb.Close SaveChanges:=True
Next f
Application.ScreenUpdating = True
End Sub
Just if anyone random was interested
Oridoll