There is only one URI stored in the database, so if the saves happen in a very short time-frame only the last one will be sent. If a synchronization action happens to occur in between the saves, both e-mails will be sent.
The API on the CD side only allows you to update a single Contact.
Any bulk updates you need to do should happen on the CM side and be synchronized.
I know you said your synchronization is broken, but despite what it may seem -- it's actually valid to have those characters in a field (just probably not what you meant to save). My synchronization works fine ...