I could be wrong but i don't see the need to bake the filter. As i see it, you just need to concern yourself with any particulates that may be in the filter. Just run some BA and oil through it to remove any particulates, then go ahead and filter your gear. Any bacteria in the filter should be taken cared of by the BA that you ran thru it and the heat shock that you put your finished product thru.
Just my thought, if i'm off base... someone chime in.