I-539 Visa Extension Question

I am really worried because my last day on my I-94 is SEP-16, and the border is still closed. On SEP-19, Colombia might open the border but it is not sure. I had a return flight booked for SEP-6 but it was also canceled.

USCIS has not answered my visa extension, they can take up to 5 months.

While they are processing your request you are allowed to stay in the country.

Should I update my I-539 application with a new letter explaining that the flight for SEP-6 was also canceled?

Probably not needed to expand it just about this flight. You will want to keep evidence of the cancellation, though. If you get interviewed or later need to tell them something else, I would mention that.

Do you think that if I overstay this is going to affect my I-130 application? Is there someone in the same situation as me? Has somebody applied for a visa extension?

You do not want to overstay, at all. However, if you are awaiting to receive their processing of your request, you are not overstaying. Copying from https://www.uscis.gov/about-us/uscis-response-to-covid-19

Nonimmigrants generally do not accrue unlawful presence while the timely-filed, non-frivolous EOS/COS application is pending. Where applicable, employment authorization with the same employer, subject to the same terms and conditions of the prior approval, is automatically extended for up to 240 days after I-94 expiration when an extension of stay request is filed on time.

OTOH, if after the extension you requested you would still need to leave by SEP-16, then you should request another extension.

You do not need to "update" anything about your cancelled flight from Sep 6 because the fact you filed an Extension of Stay already meant that you were seeking to stay beyond your I-94 expiration of Sep 16 in the first place.

You do not accrue "unlawful presence" while your timely-filed, non-frivolous Extension of Stay application is pending. Even if your Extension of Stay application is denied, unlawful presence would only start to accrue starting from the date of the denial. You only trigger the unlawful presence ban if you accrue 180 days of unlawful presence and then leave the US. So it you leave soon after a denial of Extension of Stay, you would not trigger a ban, and you should have no problem getting your immigrant visa.

But, since you are in the US, and you are seeking to immigrate since your spouse filed I-130, why don't you just file I-485 for Adjustment of Status? That way, you can immediately stay in the US instead of having to wait for the I-130's approval and the immigrant visa process in your country. In your category, you can file I-485 even if you are out of status, no matter how long you've been out of status. There shouldn't be concerns that you misrepresented yourself when you entered since you did intend to leave soon, and the change in situation was due to COVID-19 and unexpected. The only downside to doing Adjustment of Status would be that you can't leave the US while it is pending (at least not until you get Advance Parole).