I would have posted this as a follow up on the original thread but it was closed, that being said I wanted to let everyone that was interested in the reason why the price changed.
According to Anson from PCBWAY who communicated with me via email, the engineer that reviewed the order mistook a 50-boards order (2 panels) for a 50 panels order (1250 boards) and without confirming with us changed the price.
He confirmed that there was no issue with the files and other than what I reported in that thread they had asked me to eliminate the soldermask bridges for the case of when using black paint but we had already assigned to a different manufacturer so we had abandoned the order at that point.
He also said the reason I couldn't see the reason why it was increased is that they have a bug in their website code that when something is pending as in this case the request to change the soldermask bridges which even being compliant with their specs apparently the black matte can't do this type of bridges which the green can, then the pending state prevents the website from displaying the reason for the price change. So until that pending state is resolved it won't show the reason for why the original price had been increased and that's why the reason it wouldn't show it on my side. He said he requested the bug to be fixed so this doesn't happen in the future.
He also said the customer service representative instead of giving me an incorrect answer when I asked why it increased should have asked the engineer when she saw that there was no reason displayed for the price increase so she would have prevented this problem. He said they will train her so she knows how to handle this situation in the future.
He apologized for the trouble and put a $50 credit in our account as a token for the errors.
I told him not to worry that I understand that mistakes can be made and that I will give them a shot in another board. We make several boards per month so I will be sending a new one to them in a couple of days. I bet there won't be any problem because he came trough and faced the problem and addressed it professionally and that's truly appreciated.
Cheers.