Hey TinG,
It is very frustrating. We have been discussing these issues in another thread: AIMA’s new GV process - Residencies & citizenships / Portugal Golden Visa 
- Nomad Gate Community
My situation is similar to yours. The portal will not allow us to upload updated documents and so far, we do not have a response from AIMA as to when this will be fixed. I took the chance and did new criminal records and got them apostilled as it can take some time and I figure they are valid for three months. Hoping this issue is resolved before then.