hey alex,
there are different issues I guess.
first of all it´s not quite clear what source-format you´ve used to create a BD or DVD.
if you are talking about MP4-files they are not similar to BD-complient xxx.h264 oder xxx.264-files and it´s no good idea to use these files within encore.
as with ALL authorings (DVD + BD) the best way to use assets is to encode them according to DVD/BD-spec prior authoring.
meaning: use adobe media encoder to create SD-MPEG2- and AC3-files (using the DVD-preset) and HD-H264- and AC3-files (using the H264-blu-ray-preset).
take care about field-dominance, as media encoder has lower field as preset (for DVD). all NTSC-sources are lower field, but HD-source is progressive or upper field first. PAL could be upper or lower field first depending on your source-codec.
cheers
danny