I've been working on multiple projects that can have anywhere between 100-1000 scans in them. Whether using auto register or not, the best workflow seems to be to create multiple clusters of scan groups and refine them to steadily larger groups. I tend to find that I can quickly create 10+ clusters/groups of individual scans. It can become quite tedious to locate the scans when trying to combine groups or add new scans to them, especially after suspending a session as Recap likes to collate the groups and re-number them (however the numbering is sometimes irregular and non-numeric).
A nice feature would be able to run a simple search for a scan on both sides of the registration.