Thanks for the help p24leclerc but unfortunately that didn't help. However, I played around with it and it seems to be working after I made a couple of changes. Now I'm curious if someone can explain why the first doesn't work but the second does in case this comes up again in the future.
Previously, once it found an item not on my list it would just stop and loop through every file after the new file at Workbooks.Open (FilePath) even if I just pressed F8 once.
FilePath = Directory & FileItem.Name
Workbooks(OrgWb).Worksheets(OrgWs).Cells(r, 1) = FileDate
Workbooks.Open (FilePath)
'Do Suff with Open Book
Filename = FileItem.Name
Workbooks(OrgWb).Worksheets(OrgWs).Cells(r, 1) = FileDate
Workbooks.Open Filename:=Directory & Filename
'Do Stuff
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