It's hard to guess what did it. Here are things to consider:
The first thing to try, always, is to clear the Site Cache (on the Site menu), Flush Permissions, and Flush All Sessions (on the Security Menu), manually delete all files in the core/cache directory, and clear your browser cache and cookies.
If it were a permissions issue, you would normally see some kind of "access denied" message, though not always. It's possible that the user saving the resources does not have either 'save_document' permission in the Context Access ACL entry, or 'save' permission in the Resource Group Access ACL entry.
See if making the user a sudo user makes it go away (Security -> User Management -> right click on the user and select "Update User", check the 'sudo' checkbox and save the user). Then Flush Permissions and Flush all Sessions again. If that fixes it, it's a permission problem. If the resources are protected, the user may need to be added to the group that has permission to save them or the permissions in the appropriate Policy need to be checked. If you don't want to leave the user as a sudo (all-powerful) user, don't forget to undo that (flushing Permissions and Sessions afterwards).
Look at Security -> Resource Groups and see if there are any resource groups with no name or if those resources belong to another group. Resources that are not in any Resource Group are unprotected, so if the Resources are not in any group, again, it's probably not a permissions problem.
If all that fails, I would first go into PhpMyAdmin and repair all tables. Then, take a look at the modx_site_content table and make sure that the alias field for the problem resources is not empty and the context_key and parent fields make sense. The context_key would normally be 'web' (unless you have multiple front-end contexts) and the parent field should be set to the ID of an existing resource (and should never match the ID of the resource itself). Look for any other systematic differences between those resources and the ones you can save.
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