Be aware that you should always use the latest versions of both Drupal 5 and CCK 5 when you upgrade.
The recommended process is to:
- Upgrade your 4.7 site to the latest CCK 4.7 version and be sure to run upgrade.php after updating your CCK files.
- Convert your 4.7 site to the default theme (bluemarine).
- Turn off all contributed modules on your 4.7 site.
- Completely remove all 4.7 files, install the 5.x files and the files/ directory.
- Note that in 5.x, the recommended place to put contributed modules like CCK is in /sites/all/modules/ instead of /modules/. This will keep contributed modules separate from core modules.
- Use upgrade.php on the 5.x installation
- Start installing and turning on the contributed modules in the 5.x installation.
Note that if you want to import data into CCK, you may want to do that in 4.7 before updating to 5.x because many of the existing methods for doing CCK imports (like the Node Import module) have not been updated to 5.x yet.
More Details About the Update
The 4.7 version of the content module created a table called node_type to track the custom node types that were created in CCK. In Drupal 5.x, that table is created and maintained as a core file. The most recent 4.7 versions include an update to rename the content module version of this table so that the upgrade to 5.x will be able to create it's own version of that table.
If you are running the most recent 4.7 content module version and have performed all possible updates in 4.7, you should have no trouble updating to 5.0, since that table will have been renamed and will create no conflict. However, if your version of 4.7 is not up to date, you may still have a table in your database called node_type. If so, and if you are using Drupal 5 Beta-1 or Drupal 5 Beta-2, you will get error messages when you update to 5.x when the core installation tries to create that table.
The latest 5.x version of CCK will correct any errors that occur during the core upgrade by renaming the table and rerunning the failed core updates. However, it is recommended that you just avoid this problem altogether by using the latest versions of all these components when you upgrade.