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With every major Oracle roll up patch, we experience problems with missing responsibilities or other user role type problems.  What can be done proactively to maintain user roles and responsibilities.

It is difficult to answer this question without knowing which responsibilities are disappearing (e.g. standard, custom, both), but for a Workflow perspective, a good place to start is the section titled "Synchronizing Workflow User and Role Information" in Chapter 2 of the Oracle Workflow Administrator’s Guide.  Each module's patches are SUPPOSED to automatically synchronize the user and role information from the source modules with the Workflow local tables, but not all of them do so.  As a result, you can run a concurrent program named "Synchronize WF LOCAL tables" to perform synchronization in bulk after applying the patches.

If you are using a third-party LDAP user directory with E-Business, then you should investigate the "Synchronize with LDAP information" concurrent program, as described in MetaLink Note 150832.1 (Implementing Oracle Applications Synchronization with LDAP).

You will probably also need to run the "Synchronize Workflow Roles" concurrent program after patching.  Although not mentioned in the Administrator's Guide, this program is described on MetaLink, especially in Note 340513.1 (Error In Workflow 'XXXX' Is Not A Valid Role Or User Name), which you may have already reviewed.

Other than closely examining the patch to be applied and running the "Active Users" and "Active Responsibilities" reports before patching, I am not sure that there is much that can be done proactively to capture or maintain custom user roles and responsibilities, other than to use the FNDLOAD utility and the afscursp.lct config file.  More information on FNDLOAD is available in the following MetaLink Notes:
  https://metalink.oracle.com/metalink/plsql/docs/LOADERS.HTM
  Note 376469.1: Can FNDLOAD Migrate User Accounts Without Forcing Users To Change Their Passwords?
  Note 436042.1: Missing Start And End Date Records In Fnd_user_resp_groups_all