Each time you go on trip in a foreign country, some tomb contents "reset", it's normal.
It's a good deal to visit each tomb on each trip because every doors are already opened and most traps are disarmed.
BUT some item never regenerate :
- sigil relic (like the ones you are missing)
- some keys
- Pangu Axe
So, Only one characters per save can complete Pangu Axe quest and sigil relic.
If you use only one character as tomb raider in order to complete Sigil collection, the explanation is simple : you have missed them.
Some Sigil are very tricky to find, hidden behind secret doors (sometimes secret doors in a secret room).
The list pallyndrome linked you will allow you to locate corresponding tomb, and you will have to inspect walls near the end of each ones.
I just finish Egypt's collection (13 sigils to find) and the one from Abu Simbel is really the "most" difficult one to find in all 3 countries.
If you need help for a specific tomb, ask it ^^