Quoting Chris Johnson cxjohnson@gmail.com:
Agreed. Punting support for people who run multiple sites from one install with Drupal 5 is pretty bad. By the time we migrate to D5 sometime this summer, I suspect we will have 40 to 80 sites, running from 1 to 3 installs.
I would put D5 in a different directory and update sites gradually. Add D5 to the DB table prefix and copy the existing data to the D5 table space before doing the upgrade. You can point to D4 vs D5 using the httpd config files. This gives you a backout path should you need it. Then when the upgrades are complete you can drop the older tables and the D4 version.
Earnie