I suspect there were no issue in the first place. A lot of time ago, if torrent client encountered files are missing, you had to run long process of verification for them to become available for seeding.
Now, if torrents switched to "files are missing" you can restart torrent client and seed like if nothing happened. No need for categories even. Also, function "Set location" can be used to move torrent to external storage.
Why do you think Gephi is using Graphviz? I think it does not. In graphviz there is no Giant Component filter and no centrality statistics, which are part of graph theory. Gephi is closer to graph theory than graphviz is. Graphviz does have some good node placement algorithms, but in general these apps have different scope. Graphviz is a no go for this purpose.
Gephi, NetworkX or iGraph - pick single one of these and it will be a single tool you need to repeat steps in the post and achieve similar result. But latter two are programming libraries. Managing to get and launch Gephi probably worth the hassle.