I have written a SEQ<->SOE map converter script (it converts both ways) and have it on my site for the time being, though it will likely be moved to Fatal's site.

Some of the major features are:
1. Preserving colors most of the time (using white otherwise) when converting SOE->SEQ and all the time when converting SEQ->SOE
2. Rebuilding lines when converting SOE->SEQ wherever possible(like colored lines are grouped together up to 250 points)
3. Preserving point locations
4. Correctly flipping the signs on X and Y coords (though I'm still not sure if the Z should be /10 or not)

Disclaimer: I have not extensively tested this script, but it does work with the maps I tested, both SOE and SEQ.
Converting SOE->SEQ takes a *bit* longer than SEQ->SOE (due to the complexity of the SEQ format)

If you find any bugs or eccentric behavior with it, let me know here.

http://www.k-r-g.com/convert.php