@ChezJfrey, I would feel very grateful if you found a moment to examine that savefile and try to fix the problem. Next time I'll play GoF Eras though, since you say it's less buggy and has more content. Best regards.
JombloLeon
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Here's a save from the town where blueprints are missing in the shipyard.
https://drive.google.com/file/d/13axHI0gkAveE3w3WvPcbO8kUnaTAZu-_/view?usp=shari...
Here's a save file before going to Amatrice shores to fight 2 MOWs, but neither of them has the log in cabin.
https://drive.google.com/file/d/1oLi8FCjD_DNcAQnAp19bMoE8d7yMZBMC/view?usp=shari...
Luckily it's not game breaking, but annoying nonetheless. After Atila tells me to wait 2 months while he searches for Salvatore, it was optional in the stock game to return to Isabella's house in San Juan and be met with hired goons there. In Maelstrom GoF 2.5 however, they don't spawn at all and I cannot exit the house after entering it.
Over the course of 3 playthroughs once the Ascold quest Aztec tablet didn't spawn in any random cave (I even used debugger to check the location and it still wasn't there) and twice there wasn't any Spanish list in the cabins of the 2 MOWs in the same mission.
Also, a medium key was missing in COAS both on Velasco and during "Life on Esmeralda" quest which I couldn't complete because of that.