Scoping & Systematic Reviews with large sets

Is there anyone working with scoping or systematic reviews who has advice on how to deal with limitations in working with large sets? I’m especially thinking of PubMed. When you get up past 5,000 or so the number of results in the .nbib file varies. For example on a set of 7,817, I can never get all the results. I’ve chatted with EndNote support and we’ve made sure duplicates weren’t being taken out, and that the proper import was used. They get the same issue in that when they export they get different numbers, too.They seem to blame the browser, but the problem is that we pretty much all have to use browsers to interact with our databases. Anyway, It’s not so bad if you’re using Web of Science, since you can send in smaller, specified ranges (1-1000, 1001-2000), but for a database like PubMed, your options seem to be as many boxes as you can click or everything. I feel like without a good workaround, systematic rev researchers are just going to skip citation managers and go straight to export to the sys rev software. Maybe this should be in the product suggestions? Advice is appreciated.