I looked at Part imports and the field "ACTIVE/INACTIVE is not included in the import process. So there is no automatic way. (BW2013)

What my company has done in the past is break the 1,000s of parts in to groups, hire high schoolers or use interns to do the "mindless" work. There is a burn out factor. The second thing we have done, is a slight partID change; we used to "Z" parts to the bottom of the parts and those were deletable by person who had "nothing to do". I typically did those in the summer while our company was slow.

Example Partid ABCDE became ZABCDE , this helps if the part is "semi" active do to part's history data retention

PS we switched from the letter "Z" to the tilde symbol "~" because we have customers that start with "Z"

Hi Vicsoria86,
Since you were successful in renaming the part ids, if they are in a range you could set up a new product line for only inactive parts. Then you could do a global part change in IC, Parts, Global part change selecting Product line in the "Data to change" box. Please backup prior to doing any global change as there is no undo. Then you could exclude this product line in by filtering on Product Line, does not equal xxxxx. Hope that helps.
Thank you,
Janice