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I think they need to provide more clarity (and I have asked). For now, it sounds like they are not going to cover the INITIAL replacement of Gill batteries by Concorde (even if the Gills are failed) ... "you install the STC" ... but they will cover replacement of the Concordes once the Concordes fail out of warranty.
IF that is the case, you basically are out of pocket one replacement cycle to get switched over.

I would argue this point with ECC... if ECC would have to pay to replace the Gill's by contractual obligation, and you wanted to upgrade, they would AT LEAST owe for the Gills... any uplift in the cost for whatever else (STC or batts) I think the owner would have to pay for, fair enough... they are chiseling you and skating the obligation.