I believe the applicant for residency only gets a prorroga when migraciones accepts the completed application.
As far as I know, if the residency is declined they will not receive a precaria and they will have whatever time is left on the "first" prorroga to either appeal the denial, leave the country, or stay as an "irregular inhabitant."
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I just got my precaria one week ago and though my visa was expired I never got a prorroga. Here's my experience if it helps anyone:
I was applying for permanent residency because my wife is a dual citizen US/ARG.
June 23 2019 - I arrived under the 90 day tourist visa and started submitting my paperwork in August and paid the extra price for the expedited service.
I had delays getting some docs from the US and was worried my visa would run out even before my documents arrived, so I went back to the immigrations office building 6 and asked about the prorroga. The clerk told me that I could come back 10-days before my visa expires and pay the prorroga fee (something like 2,000 pesos I think) but not sooner. He also said that if I had no need to leave the country, he recommended I did not pay the fee, he said "save your money". He explained that it would only be a problem for me if I was trying to leave the country, but if I was intent on finishing the tramite to just keep going and not pay the fee.
Sept 18 2019 - I ended up getting the documents I needed and submitted my tramite only a few days before my visa expired.
Sept 30 2019 - While waiting for the next step, my visa expired. I got an email from RADEX that my marriage cert was incorrect, so I went in the system to re-upload.
Oct 2 2019 - A week later I got the same email with the same issue. I think the problem was that my marriage doc was 8 pages with apostille, translation and legalization, but they only let you upload a jpeg in this section. This time I uploaded just the translated 1st page of the marriage doc.
October 23 2019 - I received a notice to appear the following day 10/24/19 and bring my paperwork.
October 24 2019 - At the immigrations office they asked me for all the documents and I was issued a precaria that same day. This is when I believe the expedited service paid off since I was assisted by one of the managers that sits behind all the front counter attendants. I also came with an Argentine family member who insisted I spoke with the person who sent me the email. The precaria I received was set to expire by the end of the month, so I went online and renewed it easily.
October 25 2019 - I received an email to come to the office within the next 10 days
October 29 2019 - At the immigrations office I was given an appointment for my wife and I to get an interview on February 12th. I was told we would both need renewed verification of residencies and proof of income. I'm assuming this is the final step.
Throughout the process I never needed the prorroga. I was also worried that leaving the country would reset my application, since you have to be in the country to start it. I also went yesterday to a local ANSES office and got my CUIL, just showing my precaria and passport as explained in other forums here.
Thanks to everyone that has posted on this site, it really made a difference. I'm happy to share any other details of my experience.