I've had a some experience that might be instructive. We have a system written in Perl that works with a vendor product written in .Net. Flow can pass back and forth between them with all key data in the database. Issues:

• All key data must be in the database. If you are relying on anything else for processing or state that might be on the file system or in memory, you'll have to change that since the other side can't see it.
• I believe all database access in .Net is through the framework, so you won't have much control over the way it uses the database. Make sure you test and make sure it inserts and updates in the way you expect. The vendor DB we are interfacing with is poorly designed and in some cases we've had fields inserted with strange whitespace stuff at the end. This can be very confusing when trying to debug. Some tests to look at the db records before and after the new code modifies things might help.
• Be careful as you recreate shared components of your perl system. For example, if you have a share sub that does 'update_user_record' you'll probably need to re-write it on the other side. Make sure it does the same thing on both sides if they are to co-exist for a while. Again, some tests here would help you.
• Timing can be an issue for inserts on the .Net side. The implementation in our vendor product doesn't get back the results of a database commit before it passes control back to Perl. It happens when COM gets around to handling it. We had to build checks into the Perl part to check the DB and wait until the other side was done before it continued along. This could be just a problem with the vendor product.

It should be possible to live in both for a period of time, but the key people on the project will need to really understand all the moving parts of the system. It can be very difficult to support such a system as well, since there are many place to look when things stop working.

The up-side is your group will get a taste of .Net alongside Perl and be able to make some fair comparisons. You'll be able to pass up some good information on how successful the full transition is likely to be.