I can’t make sense of this whole thing. What’s clear is that you misjudged the project "back then" because you were naive. It was a bad situation, but now it can’t be changed. Why the appraisers didn’t notice that someone had been "tinkering" around, I don’t know, but of course it could be that they really didn’t notice, have good contacts with the heirs, etc. But with two independent appraisers, that’s rather unlikely. Why your appraiser didn’t discover the leaking garage during the moisture measurements is beyond me. But that’s just background.
What is clear to me is that you are a layman in the whole area (not basically a problem). But you seem to want to save the cost of an architect/construction supervisor and are now discussing the completion of individual components with various craftsmen who (logically) have little interest in finishing construction botches (at least that’s how it sounds). I don’t want to speak badly of the previous owner, as I know too few facts. But he seems to have come up with some kind of high-tech project far from any standards. I would seriously consider throwing out all the "special components" and using off-the-shelf ones. Solar thermal, photovoltaics, and storage can be wonderfully reused. The ground collectors would need to be seen. The heat pump including control should be new (if it really suits the passive house) and then you have a functioning heating system. Everything else seems to me from here like a makeshift solution that will only cost you money over the years. Someone has to maintain it anyway. Then add controlled residential ventilation and make the remaining rooms ready for occupancy. That should easily be achievable within half a year if you get a decent architect. Maybe you just went to the wrong one. Not everyone is technically savvy enough to be familiar with heating systems. Many just type their house components into their software, get their energy consumption from that, and then choose a heating system from a catalog. Most don’t delve into the technologies, let alone the controls, and therefore probably won’t be much help to you. It’s best to look for people who primarily do renovations. New buildings are much easier in this respect because you can just start according to the textbook. And €15,000 for planning the renovation seems very exaggerated to me. He can bill that later for the complete construction supervision, but in order for you to plan, you first need a renovation plan + costs, and that’s cheaper.
PS: Regarding the bank loan, it might of course be that the bank is getting cold feet. Maybe they really only looked at the house from the outside or not at all. After you have now explained everything that is still open, they may actually be afraid that the amount cannot be recovered through the sale and now hesitate to invest more money. On one hand, you have the same concern, on the other hand, you don’t exactly seem to be presenting the whole thing with optimism. From the bank’s point of view, I would also ask myself why it wasn’t possible for you to make the house fully habitable in 3 years and you only now come around wanting to take out money. On the other hand, your income is very good. That means your property may be risky, but your creditworthiness is not. The likelihood that the bank will not get its money is therefore low. Granting an additional loan that does not provide a corresponding value in return is, however, too expensive and thus unattractive from the bank’s point of view.
That, however, is only speculation. No one knows what is discussed internally at your house bank.