If YOU believe in the process and have had good results, then get it done.
I agree with you, sooner, rather then later.

My 78 300D was rustproofed with rusty Jones and was very well preserved. I live in the rust belt.

I would imagine that any warranty work that you would have done would be for mechanical issues. i do not see where they could evaporate your drivetrain warranty for rust proofing.

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1959 Gravely LI, 1963 Gravely L8, 1973 Gravely C12
1982 380SL
1978 450 SEL 6.9 euro restoration at 63% and climbing
1987 300 D
2005 CDI European Delivery
2006 CDI Handed down to daughter
2007 GL CDI. Wifes