Ngl, I ran the exact same setup for years with those cheap no-name pens and never saw a single film, even on 12 layer boards with preheat at 100C. Sounds like you might've had a bad batch or the board finish was more porous than usual, not a blanket flux issue. I've had gel fluxes leave worse gunk in vias than any pen when the solvent flashed off too fast. The chalky stuff you saw could've been baked on activator from the solder paste itself, not the pen. Trying a different brand is fine, but blaming the pen feels like a shortcut when multiple variables changed at once.

The caliche layer is probably why you missed it. That stuff hides everything, and once it sets, it makes a site look way older than it actually is. Maybe worth checking if the rebuilds used the old floor as a base, that could explain the odd rock cluster.

Question whether it's really that deep though. A PCB swap is a PCB swap, whether it cost $10 or $80. The boutique one probably just had a bad solder joint or a faulty cap, not some magic design flaw. Everyone acts like these fancy boards are fragile treasures, but most of the time they fail from basic wear or a bad batch of parts. If the cheap one works after rewiring, good for you, but that doesn't mean the expensive one was worse, it just means you got unlucky. Fixing it with a generic part is fine, but don't act like you uncovered some hidden truth about the whole market.