That does not seem to be the problem, I don't have more than 1000 Links in one category. But I tried to set the limit to 5000, but the building process stops again.

Isn't there a possibility to have a build-staggered option, where I can - such as links 2.0 - give the number of categories to be build within steps? Or to build the categories starting with the last of them.

I don't really have a clue......