I think you are tackling the problem in the wrong place. The problem seems to be with the MCU power supply section or PCB layout. Whereas you are hunting down the sources, which will change as new equipment gets added in the factory.
I wholehardedly agree

Right now I have eliminated the problem almost to a non-existent level : There was a thermostat that was switching on the cooler motor relay and that relay had no free wheel diode earlier. Now it has.

1) you do not say 'never' you say less often - once is too often.
2) Noise wil ALWAYS become more and your board MUST be able to handle it.
3) what will you do if (after 17 months) you are called "the unit fails on a regular basis" blame your customer for installing an elevator?
4) what you have done is valuable but NOT the solution.

Were I you I would remove all the noise suppression added, make the board work under those circumstances and then put the noise suppression back.

Erik