The duplicate content thing is kinda impossible to solve perfectly. Some people will tell you it’s a feature, and it can be interesting to see the different instances’ comment sections (especially after moderation), but yeah it can be annoying to have your feed dominated by a few stories.
The default web front-end will merge crossposts, but won’t if they’re multiple posts to the same URL. I think some of the apps do have that deduplication as a feature, but I couldn’t tell you which.
I remember the same problem from my Reddit days, but there wasn’t generally so many similar, overlapping communities.
Going into more detail would be helpful: Do you get an error? Do some settings restore or change? How old is your backup (i.e. from what version of Voyager)? Android or iPhone (before and after)? Are you selecting a file from your device, or trying to use from cloud storage (Google Drive, Nextcloud, etc)?