Maybe disabling this will help?

nixos/server/package-configs/conduit/default.nix

@@ -63,7 +63,7 @@ in {
   # Configure NGINX as a reverse proxy
   services.nginx = {
     enable = true;
-    recommendedProxySettings = true;
+    recommendedProxySettings = false;
 
     virtualHosts = {
       "${server_name}" = {
@@ -123,9 +123,10 @@ in {
             add_header Access-Control-Allow-Origin "*";
           '';
         };
-        locations."~ ^(/_matrix/client/unstable/org.matrix.msc3575/sync)" = {
+        locations."/_matrix/client/unstable/org.matrix.msc3575/sync" = {
           proxyPass = "http://backend_conduit/client/unstable/org.matrix.msc3575/sync";
           proxyWebsockets = true;
+          recommendedProxySettings = false;
           extraConfig = ''
             proxy_set_header Host $host;
             proxy_buffering off;