I had an odd problem that I never heard of anyone complaining about before. When I was on vacation I bought a guitar and everything was perfect in it and I loosened each string half a note up before flying back to my destination. When I arrived at my destination my guitar rattled a lot in the 6,5,4, and 3 strings. That rattling killed the sustain of the notes. Later than I realized the rattling was because the frets especially in the top low e string were jutting out more than the high e string. It wasn't like that before I went on the airplane. The plane must have put pressure on the neck pushing the glue under the frets up therefore making the frets jut out more. The fret jutting happened in the fat strings the most because there was the most pressure there. I should have completely loosened the strings before flying. So I sanded the frets to make them all an even height and that got rid of the rattling sound and the sustain came back to normal.

My question is when checking for the truss rod adjustment (the capo and 16th fret way etc) will I get inaccurate results when I adjust a neck relief of 0.3 mm since all the frets have been lowered slightly?

My other query is when cleaning the neck with lemon oil or linseed oil can the oil sink into the wood deeply enough pushing the frets up?

Your measurements won't be off. After all, your measuring the distance between the top of the frets and the bottom of the string (not the distance between the fret board and the string.

Lemon oil won't cause the frets to lift out. If it did, no one would use it as a fretboard conditioner.