According to Doc ID 567752.1, we can't use an alternate account with a different balancing segment f

We have a situation where we have merged two balancing segments into one.  Some of our vendors have still not changed their systems to reflect this and are sending us data files with the old balancing segment.  We want these automatically converted to the new combinations using a different balancing segment.  Unfortunately, this doesn't currently work and I'm trying to rack my brain as to why this limitation even exists.  Can someone enlighten me how I would accomplish what we'd like to do and why I can't use the alternate account functionality?