Misread the question. When the binary is obfuscated you need to be careful when class names/namespaces get changed etc. This will break not only between obfuscated/non-obfuscated binaries, but also between different versions generally.
This product apparently excludes classes that are marked as: http://www.ssware.com/cryptoobfuscator/obfuscator-net.htm (This is not a recommendation, I have never used - you will have to test it and see if the cost is worth it).
Apart from that you could write a custom serializer depending on how much data you are serializing.
[Original Answer]
Why are you obfuscating the data? I can only imagine it's to prevent someone for editing it or to prevent someone from reading the content.
If it's to prevent someone from editing it then can I suggest you include a hash of the data, and then don't bother obfuscating it.
If it's to prevent someone from reading it then I suggest you encrypt the data instead after it's been serialised.
There are plenty of examples of both but if you would like an example let me know.