Hi,
I'm not sure that any of the schema changes necessitated by Unity would break Unity per se. However, if there are multiple versions of Exchange with Unity subscribers' mailstores on them, then Unity must be partnered with the most recent version. In this case if there are Unity subscriber mailboxes on Exchange 5.5, Exchange 2000 and Exchange 2003 all in the same AD domain, Unity should be partnered with the Exchange 2003 server.
The tested and supported method of what I think you are trying to accomplish is covered in this link: http://www.cisco.com/en/US/products/sw/voicesw/ps2237/products_upgrade_guides_chapter09186a00806cb90c.html
I think your general plan should work, if after you perform the upgrade to Unity 4.0.5, you follow the link above to cover the Exchange 5.5 to Exchange 2003 upgrade (as it relates to Unity's connecting to Exchange).
It wouldn't hurt to take another DiRT back up after the upgrade to 4.0.5.
I hope this helps.