Hi,
Based on my (albeit limited) experience, I don't think that you should be worried about sending your lens in for a repair right now. To ensure that nothing gets lost, you will want to ship the lens with insurance (of course) and tracking. You may also want to take photos of the lens in the box and any other accessories that you decide to send with it, such as front and rear caps. I would advise against sending in anything unnecessary that could be misplaced, such as a lens case. There is room on the form for you to list all accessories that you sent in, and you can label the items that you send in (for instance "Accessory 1 of 2: Rear Cap") to make it easy for them to check if they forgot anything before re-packing their box.
In June, I ordered a 400mm DO II (new) that arrived with visible defects on the lens mount rubber. My store didn't have any others to do an exchange, so they directed me to go through Canon service, which I thought would be a huge pain. It wasn't. Apart from a longer than expected hold time to reach the service center (45 minutes), everything else exceeded my expectations.
Canon's phone team was excellent, and sent me a prepaid label since the lens was brand new. They expedited the shipping, so it arrived to them within 2 days (while traveling 3000 miles to VA since the one in CA was closed). They fixed the lens within another two days, and shipped it back to me expedited.
All in all, it took one week for them to repair the lens. For some reason, the lens suitcase arrived back with many scratches. I sent them a photo of before (it was brand new) and after (it looked like it had been through an ordeal), and they shipped me a new suitcase with no hassle (supposedly a $450 value, so non-trivial). I was glad that I had photographed everything before sending it in.
Would I have preferred to receive a non-defective lens in the first place or just get a different new one from my store? Yes, of course. But Canon's service on this one seemed like the next best thing. Excellent by any standard, and you would never have known it was all taking place during a pandemic.
I had to send in my R5 yesterday due to a faulty circuit board (hold time reduced to 20 minutes). I'm hoping for the same level of great service. This time the CA service center is open, so it may be even faster. Again, I would have preferred to get a non-defective camera or to be able to do an exchange at the store, but those options were not available.
It's a good thing that Canon's service is so good, because I've wound up needing it on my first two Canon purchases so far. The other camera brands that I have owned in the last couple of years have very poor reputations for their service, but I never wound up needing them even after shooting in very challenging environments. I'm hoping my experience with Canon gear improves from here on out, as I've purchased several more lenses and hope to switch over to Canon entirely this year.
Good luck with your repair. I think you will be pleasantly surprised.