I lost the ability to do progressive invoicing too and found that it turned off when they did the update. When I turn it back on, it works, but when choosing to invoice a percentage, the partial invoice that is created is blank with all zeros. Here are the instructions to turn progressive invoicing on, but it's still not working correctly. Does anyone know how to fix this issue?  It does say you have to use their template (which is bogus) so I may try to switch to it, but shouldn't have to... I like my custom invoice and my customers expect it! Do better QB!

Here are the instructions on how to turn it on... 
1. Go to Account and settings.
2. On the Sales tab, go to Progress invoicing, then Edit .
3. Turn on Create multiple partial invoices from a single estimate.
4. Save.