I figured out that the first entry in upgrade.2da wll dissapear on area/load/save transitions (that appears to be the cause of the dissapearing Rubat crystal I've been posting about). So my solution is to insert a blank entry at line 0.
I've been fooling around with TSL patcher to post a patch to do this, but can't insert a line. I've resorted to having it simply change line 0 to a useless entry and make line 203 (the old Rubat line that had a Z added to make it do nothing) the entry for the Rubat crystal. However, being a stickler about changing as little as possible, it bugs that I might be messing up the sort order on the upgrade selection screen (I know, nobody but me probably cares). I don't know if simply changing the "Row Label" will alter the sort order (so I can maintain the original order in wich the crystals are displayed).
Anyway, there you go; a use for inserting rows at places other than the bottom. I'll probably just say screw the sort order and set it up the way I described, though I thought I might mention it as a potentially usefull feature to add.