Combining hand-routing and auto-routing in Eagle; selective ripup in an Eagle ULP
I hate answering my own question, but here I go. I hope I don't get get points for answering, that would be weird, only for accepting an answer? (BTW, I did not get any response on the Element14 forum.)

The solution is to use the DRAW command, not ROUTE. DRAW will place a wire segment, exactly where you specify (unlike ROUTE, which tries to connect to an unrouted airwire. ROUTE is essentially useless in a script.). The next issue is via's: I can't (or don't want to) distinguish between a manual via and an autorouted via, so I keep all via's that connect two (or more) manual wire segments. Other via's are deleted.

So what my final script does is:

prepare a ripup command
for all copper segments that are not 0.01 wide (the width I use for autorouting)
   check both endpoints for a via at that location
      prepare the via to be resurrected when it is visited the 2nd time
   prepare a command that resurrects the copper segment
execute the prepared commands


Note that it will probably not work for more than two layers, nor for other things than wire segments at the copper layer. 

IMHO the whole concept of the eagle ULP and command languages is troublesome. An ULP runs in a read-only environment, the only way it can affect the circuit, board or library is by creating a list of commands. This eliminates some useful programming techniques, but worse is that the commands were not designed to be easily created from an ULP. You need all kinds of transformations (in this case: coordinates, shape names) to translate from the ULP world to the CMD world.

(edit) Before you run this ULP, set the 'wire bend' selection to allow arbitrary angles, otherwise eagle will try to adapt the resurrected wires to the allowed angles, which can result in a bloody mess. IMHO this is another example of the problem with ULP/SCR.

This is the ULP code:

// gather the commands that must be run on exit
string RunOnExit = "";
void cmd( string s ) { RunOnExit += s + "\n"; }

// return an x or y position in the form that can be used in a command
real f( int x ){
   board( B ) switch( B.grid.unit ) {
      case 0: return u2mic(x);
      case 1: return u2mm(x);
      case 2: return u2mil(x);
      case 3: return u2inch(x);
   }
}   

// return the string form of the a via's shape
string sn( int x ){
   if( x == VIA_SHAPE_SQUARE )  return "square";
   if( x == VIA_SHAPE_ROUND )   return "round";
   if( x == VIA_SHAPE_OCTAGON   ) return "octagon";
   if( x == VIA_SHAPE_ANNULUS   ) return "annulus";
   if( x == VIA_SHAPE_THERMAL   ) return "thermal";
   return "unknown-via-shape";
}

// count the number of times x occurs in s
int n_ocurrences( string s, string x ){
   int i, n = 0;
   while( 1 ){
      i = strstr( s, x );
      if( i == -1 ) return n;
      s = strsub( s, i + strlen( x ));
      n++;
   }
}

// add a via, but only when it is visited the second time
string via_list = "";
void add_via( int a, int b ){

   // for all via's
   board( B ) B.signals( S ) S.vias( V ){

      // if the via is at the current location
      if(( V.x == a ) &amp;&amp; ( V.y == b )){
         string s, coo;

         // the coordinates of the via are used as its identification
         sprintf( coo, "(%.6f %.6f)", f( V.x ), f( V.y ));         

         // if this is the second visit to this via
         via_list += coo;
         if( n_ocurrences( via_list, coo ) == 2 ){

            // resurrect this via
            sprintf( s, "VIA '%s' %f %s %s;", 
            S.name, f( V.drill ), sn( V.shape[ 1 ] ), coo );
            cmd( s );      
         }
      }
   }         
}

if( !board ){
   dlgMessageBox("start this ULP in Board", "OK");
   exit( 0 );
}

board( B ){ 

   // first delete all coper segments, 
   // later we will resurrect what we want to keep 
   cmd( "RIPUP;" );

   // for all wire segments in the top and bottom copper layers
   B.signals(S) S.wires(W) {
      if( ( W.layer == 1 ) || ( W.layer == 16 ) ){ 

         // that are not 0.01 width (that is what the autorouter uses)
         if( f( W.width ) != 0.01 ){
            string s;

            // resurrect via's adjacent to this wire segment
            add_via( W.x1, W.y1 );
            add_via( W.x2, W.y2 );

            sprintf( s, "CHANGE LAYER %d;", W.layer );
            cmd( s );      

            // resurrect this wire segment                 
            sprintf( 
               s, "WIRE '%s' %f (%.6f %.6f) (%.6f %.6f);", 
               S.name, f( W.width),
               f(W.x1), f(W.y1), f(W.x2), f(W.y2));
            cmd( s );   
         }   
      }
   }
   // dlgMessageBox( RunOnExit, "OK");
   exit( RunOnExit );
}