Yes, libraries can be prepared using 0.1-200 ng FFPE DNA inputs. The DNA should be sheared, and the libraries should be constructed according to the EM-seq v2 Manual. PCR cycles may need to be optimized, but we recommend increasing by at least 2 cycles.
Note that libraries prepared from FFPE DNA may have higher methylation backgrounds in the CHH and CHG contexts. However, using a 3C filter (available in the Bismark pipeline) or similar reduces background. The filter removes reads that contain 3 or more consecutive unconverted Cs in the non-CpG context (i.e., CHG/CHH).