I've run into this before. My solution was to find port handles and reconnect. I'm not sure if there is an easier way.
Here's a function that should do the trick:
function removeAndReconnectBlock(blockHandle)
%Get port handles and parent system
portHandles = get_param(blockHandle,'PortHandles');
sys = get_param(blockHandle,'Parent');
%Get source port
srcSignal = get_param(portHandles.Inport,'Line');
srcPort = get_param(srcSignal,'SrcPortHandle');
%Get destination port
destSignal = get_param(portHandles.Outport,'Line');
destPort = get_param(destSignal,'DstPortHandle');
%Remove
delete_line(destSignal);
delete_line(srcSignal);
delete_block(blockHandle);
%Reconnect
add_line(sys,srcPort,destPort)
Note that this only works for single input, single output blocks, but I'm sure you could see how you would extend it further.
