Today I migrated my iPhone 3gs to the iPhone 4s. As part of this process, I first had to upgrade my iPhone 3gs to the new ios5 software in order to ensure a seamless transition.
The upgrade to ios5 on the 3gs was seamless.
When restoring the backup from the old 3gs to the new 4s, which is the recommended process for migrating to a new iPhone, I lost 6 transactions. On my old 3gs, I have 8 transactions. On the new restored 4s, I have only 2 transactions. All of the 6 lost transactions were from earlier in the day of the migration to the new phone.
I am using Mac OS X 10.6.8, and YNAB for iPhone v1.4.0 (76).
Probably the easiest workaround is to recommend to users that they sync before upgrading. I can still do this with the old phone. Just letting you know.