Thank you for the replies.
My first doubt was also cam chain tensioner. Altough after removing the cam chain cover everything was fine, chain was properly under tension and no issues visible.
After that removed the gas tank and cam cover, timing signs on cams and crank were correct, no way the chain could have "hopped over a tooth". Measured the valve clearances and all were correct, in my opinion this should already indicate a bent valve ???
Just in case got a brand new OEM cam chain tensioner from local dealers stock, installed and assembled everything again. Sound was still the same so problem not found.
Next step removed the sump and found lots of aluminium particles there, frightening but at least tought now i am on to something...
Dropped the engine a couple of cm to remove the cylinder head, pistons and valves were fine, no sign of contact between them.
Then removed the engine from the frame, took it apart and removed the connecting rods from crankshaft. No it was getting weird since there was no damage at all on pistons, crankshaft main bearings or connecting rod big end bearings. Didn't remove the pistons from the connecting rods, since the CR upper bush was moving smoothly and tight.
Main bearings and CR lower bearings were visibly fine, however just to be sure measured the clearance with plastigauge method, result 0,025 mm which is totally normal acoording to manual.
Now it was clear the aluminium particles found in sump had to be there already earlier. Later figured out that last owner had broke the clutch so bad drum was also broken. Since all the aluminium parts were not damaged, this pieces had to be there since clutch breakdown (approx 8k km earlier). He didn't remove the sump so this makes perfect sense that some pieces remained in the engine.
Every corner and shaft inspected, no sign that these aluminium particles could have made a damage in the engine. Measured the piston ring gaps, matched with manual normal values. Measured cam chain length, also in limits. Checked the oil pump thoroughly according to the manual. Made a leak test to cylinder head by turning it upside down and pouring gasoline on the valves, no sign of leak.
It was really strupid feeling to assemble the engine without finding any issue, but best hope was that the aluminium pieces were stuck between some moving parts and this caused the mechanical sound.
After full assembly and firing up the engine..still the same sound, no changes.
Only thing still undone is removing the valves from the cylinder head. Is there any chance the issue is there if we now that there is no leak and valve clearances are correct ?
Damaged/broken spring etc?
To sum up what has been checked:
Valves and pistons have no sign of damage (valves not removed from the cylinder head)
Cylinder linings have no sign of wear or damage
Connecting rods, crankshaft, main bearings and big end bearings have no damage and clearance measured with plastigauge
New cam chain tensioner, cam chain measured and fine, chain under proper tension
Timing correct (has been checked after several engine starts and still correct)
There is one theory that 3 rd cylinder suffered cold stress after falling in water, cylinder shrinked with sudden cool down and damaged the piston. Piston was visibly checked but not measured or inspected deeper with a magnifying glass from microscopic cracks. This is a thing that occurs on BMW-s, so potentially possible according to my mechanic.
Forgot to take pictures of pistons, crankshaft and connecting rods sadly, added a picture of cylinder head after grinding.
Open to any ideas what to still check, really frustrating and complicated case for even real experienced mechanics.
Pieces in the red cap were the biggest foundings from the sump:

Cylinder head after gasket surface grinding.



