Quoting Brian Choc bchoc@t4tcolorado.org:
I found that disabling modules during minor upgrades causes data loss consistently under specific circumstances, during earlier updates (e.g. 5.2, 5.3). I observed that any module-supplied node type would drop all the data in any assigned CCK fields when disabling & upgrading. For example, if one had a simplenews node with an "editor" cck field attached to it, one would lose all "editor" information. However, the basic simplenews node data would be kept, as would any cck fields attached to standard nodes. Only the combo of cck + module-supplied-node-type seemed to cause problems.
So what you're indicating is that modules implementing hook_node_info will loose the node_type row and thusly the nodes of that type. This would then be a critical bug in the core base system. Or perhaps your incident is related to only one of the CCK fields modules and then the critical bug would lie with that module. Disabling a module should not under any circumstance cause data to be removed.
That said, I do not disable modules either when upgrading from Drupal version 5.x to Drupal version 5.y. However, that isn't the documented method and the documented method needs to work.
Earnie -- http://for-my-kids.com/ -- http://give-me-an-offer.com/