The second error: "[DM_SYSOBJECT_E_CANT_CHANGE_PERMITS]error: " -- has been fixed in SP3 and there is also a hot-fix available with HPSupport which can be applied to SP2/SP1 - you may want to check with HP support for hot-fix.
The first one, [DM_SYSOBJECT_E_NOT_LINKED]error I am not sure of - even we have been getting that since last day so if you found any breakthrough do share!
But we have around 300 projects, 120 proposals and 40 requests. And each of them have several attachments. So applying this workaround to all these, will take a lot of time. I am following with HP Support.