I chanced upon this post while looking for a solution to a similar error. We have hit the 2^32-1 limit and all our feature classes has at least one column which is NUMBER(38) and that column is also the primary key.
It appears to affect ArcSDE & ArcGIS. like you stated.
I cannot change the NUMBER(38) to some thing else. A lot of procedure we have, assumes that this is a NUMBER(38). Is there any other way to get around this limitation? I can re-generate the layers, if I can somehow directly map a specific column to use SE_INT64_TYPE. Is it even possible?
Thanks for your help.