Try:
Sub Confirm()
On Error Resume Next
With Sheets("Check sheet")
c_count = WorksheetFunction.CountA(.Range("C6:C99"))
d_count = WorksheetFunction.Count(.Range("D6:D99"))
If c_count = d_count Then
MsgBox " All updated"
End If
End With
End Sub
In the attached I've changed Count to CountA in the code since in column C you're not counting numbers but non-empty cells (Sheet names).
Column D contains dates so they'll be numbers so I've left that as is.
I've put temporary formulae in cells H6:I6 just to show you, delete them after you've seen what happens when you change H6 fromula from =COUNT(C6:C99) to =COUNTA(C6:C99).