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I am 37. I used to have long and sometimes hilly rides with an awful bike fitting/cadence, no hydration, no cooling down, etc. because I didn't know about all this stuff when I started as an amateur. As I started to ride longer and harder, one night I had some swelling and terrible pain on my knees. Then those pains became persistent. I was having them after each and every ride. I was thinking what I was doing wrong, but I never figured it out or it was too late because the damage was so big. Weird thing is I was riding pain free but just after few hours I get back to home I was having these nasty pain around my knees which was lasting for few days. At some point I was having knee pain even when I was sitting, walking, lying on bed and many days I woke up with pain on my knees even though I had stopped riding completely. I thought it was going to stay with me for lifetime but one day I had a crash on my motorbike and broke a bone on my ankle. That was a shock on my system I guess and my body forgot about my knees completely. All the pains had gone for the good and I am still almost glad that I had that accident because my life was so miserable with those knee pain and I had no solution having seen so many doctors, physios, injections etc. Maybe it was the long resting period because I didn't even get out of the bed for about 3-4 months.
Now I want to ride again but it seems impossible because when I try to have a ride with the easiest gearing and only 2-3 km long I end up having these random kneecap pain on both knees but they disappear next day. I envy those people who rides competitively even in their 50's.
Is there anything that I can do to do
at least 5 to 10 kms rides pain free?
Btw I am so skinny that I have almost no muscles on my thighs and became weaker after the crash because I have some atrophy on my right leg.

My sister has the same problem

You should definitely consult an orthopedic doctor. Only he will be able to understand what is happening with your knee and give recommendations or prescribe treatment. I also enjoy cycling and often ride long distances. To fix your muscles in the right position and evenly distribute the load on them, I use sports tape and I strongly advise you to do this in the future. And of course, the wrong height of the bicycle seat and incorrectly selected shoes can also cause pain and injury. But you need go to the doctor.