This update is a complete rewrite of TransportPipes, which will increase performance and FPS a lot.
The new / replaced features can be read about in the wiki: https://github.com/RoboTricker/Transport-Pipes/wiki
To migrate from an older version of TransportPipes, first of all you have to delete the TransportPipes configuration folder so that it can be autogenerated again (the config structure has changed).
After starting the server with the new plugin, it will automatically migrate the old pipe save files in every world to the new ones (which are called ducts.dat). If you're sure that the migration process has succeeded, you can safely delete the pipes.dat file because TransportPipes doesn't need it anymore.
If you encounter any difficulties especially because you are used to an older version of TransportPipes, I'd highly recommend reading the wiki again.
For example the golden and extraction pipe filtering system slightly changed in a way that you have to reconfigure the filters in order for them to work properly.