Indeed, an upgrade should NEVER do that. They dun goofed bad, and I hope there was a backup.
First, always make a backup before starting an upgrade. Check with the developers for any third-party modules and templates to make sure they're compatible before starting the upgrade. And for source-mods, check the patch ZIP to see if a modified file will be overwritten. If so, make any changes to the new file. Then follow all the instructions in the docs and the upgrade script.
In the case of 7.1.5, only about three system files are modified, and these are usually not used by mods. So if this is a 7.1.4 site, it shouldn't be a big operation. There are no database or file changes for modules.
For Trident, there's no ETA, as work re-focuses on Dolphin. As they are different scripts, there's no direct upgrade path, but BoonEx has said that a migration script is planned, so most data should be able to be transferred from a Dolphin to Trident site.
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