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For completeness:
I settled on the following small change to the above script. This allows a one hour window to complete adding the newly created kepub's to calibre's database.
$ts = New-TimeSpan -Days 0 -Hours 1 -Minutes 0
$library = "D:\Calibre_Library\"
$curdate = (get-date) - $ts
D:\kepubify\kepubify-windows-64bit.exe --calibre --update --inplace "$library"
dir -Path "$library" -Filter *.kepub -Recurse | Where-Object { $_.CreationTime -gt $curdate} | %{calibredb add -m 'ignore' $_.FullName}
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