Repeatedly getting folder with question mark after closing my macbook pro

The SSD in your laptop is failing.

I'm guessing you have the non-touchbar model with just two Thunderbolt ports. The SSD in that particular model has an extremely high rate of failure which is usually exposed when powering on the system or waking it from sleep.

I hope you have a good backup of your data because that SSD could fail completely at any moment. If you don't have a backup, then do a backup immediately if the data on that SSD is important to you.

from linked Kernel Panic report:

panic(cpu 0 caller 0xffffff801322681e): nvme: "AppleS3XController. PCI link down.

This confirms my suspicions....I've personally seen this and similar panics associated with bad SSDs while supporting my organization's Macs.

nvme  == SSD
PCI link down  ==  indicates the SSD is not communicating with the system

Plus the Kernel Panic listed a MBPro 14,1 which is the MacBook Pro 13" (2017) non-touchbar model.

I don't recommend spending any money on repairs to any 2016-2020 Intel Mac with USB-C ports for multiple reasons (2017 model has multiple design & manufacturing defects with the non-touchbar model having other lesser known issues as well such as SSD failures). The money spent on repairs is much better put towards a new laptop.

"Repeatedly getting folder with question mark after closing my MacBook pro: [...] on. I was able to upgrade OS first to Monterey and then to Ventura, which I think is the latest OS that my macbook can handle. Then today I closed the laptop again, and when I opened it, there was the folder with the question mark again. I restarted, chose my user account, and all was fine again. I got the diagnostics from Apple but additional text will not let me attach it[...]"

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Sytem Files Are Missing:

So, Reinstall the macOS:

Go Here: How to Reinstall macOS from macOS Recovery - Apple Support. Important: Be certain to create a backup of your Mac prior to all of this. That way, you can have something to restore from the Mac from, should anything go wrong with the reinstall. Once reinstalled, try this once more.