The information seems to be encoded in the visit = (hash), (flagbits) entries in the 'Player' section. There are base_visited, sys_visited and holes_visited entries in the 'mPlayer' section but apparently their only purpose is for statistics display, similar to shiptype_killed.

If you copy the block of visit = (hash), (flagbits) entries from a savegame that has seen all to a new just-before-mission-1 savegame then you get all the info on the nav map and all the prices but the player info screen will still shown bases/systems visited as 1. If you want the statistics display (player info screen) to be correct then you need to copy the base_visited, sys_visited and holes_visited blocks as well.

I have not been bored enough yet to figure out what the flag bits mean but it stands to reason that the various types of entities can have different degrees of 'visited-ness'. For example, a base will show up on the nav map once you have been near to it (less than 10 km away) but the prices won't show up in the traderoutes list unless you have landed on the base or paid an informant.

Note: it is easier to make sense of the savegames if you know a bit of .ini lore - there is a wealth of information in the editing/modding forums. Also, posting a topic like this in one of the editing forums might elicit more responses because the problem is so closely related to general FL editing/modding. Also, JohnSteve has done some work on savegames specifically and posted some information yesterday in the thread Save game file information.

Two other easy edits that can be fun: you can transfer a ship including cargo, equipment and weapon group settings from one savegame to another if you copy the block of lines beginning with 'ship_archetype =' up to, but not including, the first 'visit =' line. And deleting all 'locked_gate =' lines (not the 'npc_locked_gate' things) will get rid of those annoying 'Access denied.' messages from jumpgates and jumpholes (but the game locks some holes/gates again during some story missions).