Massimo, I'm sorry to say, but if it's really a problem with Sat2Chart, then you're probably going to have to
work around it. While Sat2Chart is a good automation
engine, it has a few issues. We'd LOVE to fix those, & to continue development of Sat2Chart with some additional features we & others have thought of, but so far, Paul hasn't let us do this, & now he's not even looking into any issues himself.
In your case, if merging multiple mbTiles isn't working, I'd suggest making your download areas bigger, & simply creating bigger mbTiles that way. SAS won't download tiles for places that are already in its cache, so creating polygons that cover areas you've already downloaded shouldn't slow things down much. In fact, I'll often rerun my downloads, just to make sure that everything I want is already in my cache, & that there are no holes from download errors.
The way I make my final mbTiles is that I don't use ANY of the mbTiles that are created by Sat2Chart in the download process. Instead, after I've finished my download process, I create BIG polygons that cover my entire area of interest. This usually includes areas that I'm not as interested in, like
interior land & mid-ocean, where the cache only has low-resolution data, zooms 10-12, but that's OK.
I then create just a few big mbTiles, at zooms 10-18, directly from the cache. SAS will put in what data it has, but I tell it not to download any more data. This gives me a high-level overview of land & ocean, & also includes all the coastal detail that I've downloaded earlier, which is exactly what I want.