You will have to create Absences in 2001 in order to reduce the Entitlement. So if you can bring the data into Infotype 2001 from your external Time System, you can still use FMLA Workbench.
We wrote a custom ABAP Program which would look at the FMLA Record on Infotype 672 and create Unpaid Absences on Infotype 2001 just to reduce the entitlement.
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