Is it possible to partially use RNeasy 96 plates and use the plate multiple times?

Yes, it is possible to use partial plates. Unused part should be taped off, so that no air will be sucked through the empty wells. That serves to ensure that you get a decent vacuum, to prevent generation of more fines, and also to avoid contamination issues. The Tape Pads (5) : 19570 can be used. Solid adhesive sealers can cause problems and should be avoided. The plates can be reused 3-4 times.