Matt,
<<Question: I have an IFR-certified GPS in my aircraft. Is it required that I
make an entry into my aircraft's maintenance logbook every time I update the
database?
Answer: Yes. The FAA, under 14 CFR Part 43, Appendix A, defines what is
considered to be a major alteration, major repair, and preventive.....>>

My answer is no.  It turns out that Part 43 does not apply to Lancairs(kits).  If you read the first section 'Applicability', you will see find that experimentals are excluded.

(a) Except as provided in paragraphs (b) and (d) of this section, this part prescribes rules governing the maintenance, preventive maintenance, rebuilding, and alteration of any*.......
(b) This part does not apply to any aircraft for which the FAA has issued an experimental certificate, unless the FAA has previously issued a different kind of airworthiness certificate for that aircraft.

I had a long talk with my FSDO and insurance company about this when I changed out my cowling.  The test they are applying to determine if you have made any "major alteration" lies in 21.93

21.93
(a) In addition to changes in type design specified in paragraph (b) of this section, changes in type design are classified as minor and major. A “minor change” is one that has no appreciable effect on the weight, balance, structural strength, reliability, operational characteristics, or other characteristics affecting the airworthiness of the product. All other changes are “major changes”

Given 21.93, your data base update is safe.  One should understand how the local FSDO interprets "appreciable effect".  If they believe part 43 is applicable, I would ask how they come to that conclusion given the experimental exclusion.

Chris Zavatson
N91CZ
360 std
www.N91CZ.com