If you have your own SSRS report server, you should create a backup of the RDL files during upgrades or other significant changes so you can make sure to retain your custom reports. If you just have a few reports, you could download them manually.
If you have a lot of custom reports and a complex folder structure, you could consider using this CLC powershell script, which would also allow you to move the reports (but not any subscriptions) to a new server.