To correct this you have to run the K2 Setup Manager in configure mode and on the Web Site Configuration step either select "Use an existing Web site" (if required site already exists) or "Create a new Web site". It is recommended to merge all split sites into the K2 site (this configuration is created by the Setup Manager by default), unless there is some very specific reason to have the sites split.
Please complete these steps (pre K2 Five installations with two separate installers):
1. Start the K2 Blackpearl Setup Manager
2. Select Configure K2 blackpearl
3. Next, select Reconfigure K2 Server Farm
4. On the step "K2 Workspace Web Site Configuration" select or create the required site
5. Complete configuration process
6. Start the K2 SmartForms Setup Manger
7. Select Configure K2 SmartForms
8. On the step K2 Designer Web Site select or create the required site
9. On the step SmartForms Runtime Site Web Site select or create the required site
10. Complete the configuration process
11. Repeat the steps above for each server within the farm
12. Verify that the farm works fine and delete old/unnecessary sites in the IIS management console.