Blesta gives PayPal a unique URL to post each IPN notification to so that the payment can be correctly applied. The URL contains the company ID, along with the internal client ID. This allows payments to be applied correctly even when the same person may have multiple client accounts, even across multiple companies.
The issue is one we've discussed internally in the past, and I believe there were limitations to being able to make this work without re-creating the subscription. I suspect it may be possible by creating a file that acts like a proxy, taking the IPN request, and determining the internal Client ID and company to apply it to. Proxying the response back to PayPal.
I'll bring it up again on Monday. If you have information about what URL PayPal notifies on whmcs installations, it may be helpful. I would really like this to work out of the box, as it removes an obstacle for migration.