Hi Alison,
Following on from Lauren's idea I think you could use Datalink to copy forward the prior months table so...
Table 1: upload this months new file, appended with table 2, apply the remove duplicates
Table 2: copy forward of last months' Table 1 using Datalink.
You should be able to rig Table 2 up using the information in the Apptio Connector Guide. Also you can schedule it so it should be fully automated.
Let me know how you go.