It seems that the vehicle replacer will send vehicles to the original depot at which the vehicle was made, even if that depot no longer exists and even if "send to home depot" is not selected. The vehicles don't seem to go to the nearest depot at all.
What it will do, it seems, is that the convoy will get sent to where the original depot was, then if it was not there, either go to the nearest depot or continue on with its journey. This results in some grid lockups if there is no road at all where the original depot was.
doing a replace on some of the passenger lines in this save results in vehicles getting stuck and doing other strange things.
http://dl.dropbox.com/u/17111233/shiki%209.12%20182x.sve
2 more bugs with the replacer
1) when a loop line is replaced, the convoys with the 'alternate directions' is not applied and all convoys will go around in the same direction.
2) vehicles are retained in the depot when not instructed to and it's a bit annoying having to sell off all these convoys at once.
(http://i199.photobucket.com/albums/aa131/AEObikes/simutrans/simscr62.png)
I had also noticed the second of the bugs to which you refer, but cannot reproduce it in the latest 10.x builds. Although I am not quite sure what has got rid of it, it seems to have gone. The "alternate directions" thing I have not yet had a chance to test - you couldn't have a go with the unofficial 10.x pre-release binaries from this (http://forum.simutrans.com/index.php?topic=7729.0) thread and let me know, could you? Note that you should not save your game using those binaries, however, as the save game format is liable to change between now and release (and has already changed since the binaries were compiled).
(Alternatively, if you can compile the code yourself, try it with the latest code from the 10.x branch). Thank you for your reports!
I think that this has probably been solved in 10.0 - can people confirm before I move this to "solved bug reports"?
The bug where all convoys attempt to go to their build depot appears to be solved and all convoys go for the nearest depot.
The bug where alternate directions are ignored upon replacement is still there.
The bug where vehicles are retained in depot, despite not enabling the option is solved.
Thank you for the reports! I shall have to work on fixing the remaining bug.