Not sure if there is something changed in the firmware with the replacement sensor, but the old method did not seem to work despite numerous tries. I did happen upon a procedure that did work.
1) Format a card in the camera
2) Check that 'Folder Management' reads 'LEICA'
3) Reset Folder no.
4) Make a picture. It should read L1000001.
5) Turn off the camera and remove the SD card.
6) Insert the card into a reader or your computer.
7) Navigate to the card, then to the DCIM folder. Rename the 100LEICA folder with the prefix number you wish. I use the first two digits of the camera serial number, so '390LEICA'
8) In that newly named folder, rename the picture file number. In my case 'L3900001'.
9) Eject the card from the computer.
10) Insert the card in the camera and make a picture.
11) Hit 'PLAY' on the camera, then 'INFO' to check that the new image is numbered correctly. In my case it should read 'L3900002'.
This was a lot of trial and error to get me back to numbering keyed to the camera. Hope I save someone a few handfuls of hair.