As far as we know, the only program capable of MPE to FLV conversion is Adobe Premiere Pro. There may be other programs, but this one definitly works.
Convert MPEG movie (Motion Pictures Experts Group) to Flash video file.
We found 3 software records in the database related to .mpe to .flv file format conversion.
Microsoft Windows software - convert mpe to flv on Windows
A timeline-based video editing software from Adobe
Convert from mpe file format
The tables with software actions are a good pointer for what a certain program does with various file types and often may give users a good hint how to perform certain file conversion, for example the above-mentioned mpe to flv. However, it is not perfect and sometimes can show results which are not really usable because of how certain programs work with files and the possible conversion is thus actually not possible at all.
A multimedia converting tool for Windows
Video capturing software from Nero Suite