The solution can be centrifuged at 13,000 rpm for 15 min.(2 to three times) and Ag NPs were collected after removing the supernatant and re-dispersed in ethanol for future use.
They will aggregate in the dry form as sure as night follows day. You'll change the form of the material by drying - they may be amorphous in nano suspension but then crystalline in dried solid form. Why do you need to do XRD? If you say 'to identify the phases' then the phases in the dried form will, in all probability, not be the same as in the stable colloidal suspension. You're altering your material in order to take another measurement... See also (registration required):
My opinion is by purification the obtaining silver nanoparticle solution by centrifugation at 12,000 rpm for 20 min. After that you can freeze/drying the purified silver nano particles, the structure, composition, and average size of the synthesized silver nano particles can be obtained and characterized.
I think the best option to get pure un-aggregated silver nanoparticles by using the centrifugation method (you can find the time and rpm of rotation in any standard literature). Another thing I will suggest, in the future, when you prepare this type of nanoparticle use some surfactant to avoid the agglomeration problem.
Badawy, Amro M. El, Todd P. Luxton, Rendahandi G. Silva, Kirk G. Scheckel, Makram T. Suidan, and Thabet M. Tolaymat. "Impact of environmental conditions (pH, ionic strength, and electrolyte type) on the surface charge and aggregation of silver nanoparticles suspensions." Environmental science & technology 44, no. 4 (2010): 1260-1266.