Thank you very very much, Gale!
I already saw all that documentation about FLAC (top to bottom!), and I didn’t find anything to keep (keyword here) what there is there already, which is what I want, because I’m using this on a chain in hundreds of files.
That option you refer only allows to add new tags, but since I’m processing it automatically in a chain, I can’t know that through Audacity in order to pass that info to the external encoder. 
In fact I’m already padding with the option you mention, as I said on my first post here. But I’m having to do it outside of Audacity - I’m using the FLAC encoder through MusicBee, which allows us to create any command line and pass it to the encoder, while keeping the current tags. So it is possible to do it, but I don’t know how. Perhaps it’s the application itself that is doing it, that’s why I was asking for a method to do it using Audacity.
It would allow me to do all my processing in only one step, instead of at least two. 
That would be appreciated, thank you in advance. 
No I don’t. I really mean the Audacity application. It’s “portable” because I decompress the .exe and overwrite the originals. And it was never installed on this system, because it does not need to. Don’t worry, there’s nothing wrong with this. I took care of personal folders registry and the likes (I’m an IT professional). I just need to copy all the structure of a previous installation, which was done only once. I do this with many apps, and it works well with Audacity and many apps like this. 
All in all, I think I will have to continue doing things the way I currently do it.
- Do the audio processing (Trim Silence, Normalise, etc.) with Audacity and export to Wav
- Apply WaveGain
- Export to FLAC adding padding with MusicBee
- Finally, add all the tags with Mp3Tag from the original version, before processing.
Since I foind out that the ReplayGain Plug-in is now automatic, I was willing to givbe it a try.
And if it works the way I need it, I would be be able to do all of this in only one step if I could keep all the tags!
So, that’s why this is important. I could save me a lot of time by automating it to 100%. 
But I can live with it… 
Anyway, thank you for your brilliant work and help. 