Jester <email@example.com> wrote this for the last update: Conversion between mod formats and especially conversion from/to non-mod music file formats is pretty sure to lose some information of the original piece.
In most of the cases, there is no way around this. You can't, for example, convert a 16-track S3M using Qxy and excessive volume commands to a 4-track M.K.. The M.K. just can't hold the information. It is possible, on the other hand, to convert a M.K. to S3M very accurately. There are a few minor incompatibilities, but these would hardly be noticeable by many. Conversions to and from MIDI are also very difficult to get done right with today's mod formats. MIDI files, while seemingly similar, have a very different command set from mods. Only one of the differences is that the MIDI output device 'knows' how to process its sounds when it receives commands from the MIDI file/player, for example how fast to decay a piano waveform.
This information is not stored in the MIDI file itself, but a mod would have it included. A converter has no means of asking the MIDI device how it would handle a certain situation (this is not completely correct, at least when using a GUS, the patches could be parsed), so it has to assume certain things. I suppose, however, that better converters could do the trick if they were programmed for certain situations (I think a converter that creates mod instruments by itself from a GUS' patches, for example, could accurately convert from MIDI to an advanced mod format such as S3M, XM or ULT).
But did you want to know any of this?
Once again M. Linus Larsen <firstname.lastname@example.org> has helped to track down some links and information in this section.