The old version of RESTClient uses SQLite to store all your requests and custom headers. However the new Firefox only supports Web Extension which has no access to SQLIte database anymore. I cannot find a way to transfer old data from RESTClient 2 to RESTClient 3. You can export your requests from RESTClient2 then import to version 3. But you have to transfer custom headers manually, really sorry about that.
Could you provide more details about the problem of losing custom headers in version 3? For example, what's your Firefox version? Are you using mac or windows? I'll try to fix it in the next version.