using upgraded speakers

Your profile states you own Play:5 (Gen 1)'s. These can only work on Sonos S1 software and with de Sonos S1 app. They cannot be commanded by the S2 app and cannot be grouped with devices running S2 software: https://support.sonos.com/s/article/4786?language=en_US and https://support.sonos.com/s/sonos-s2-overview?language=en_US

full history:

I owned 2 Gen 1's, one broke and I was offered a new Gen2 to replace it.

+Since than I bought a second Gen2.

=Total of 3 series 5 speakers.

Wanted to go to S2, but needed to replace the Gen1. Took up the offer to get two brand new series 5 Gen2 by upgrading my existing two series5 gen2. I was expecting the existing Gen2 series 5 to continue to work, ending up with 4 series 5 gen2 speakers. I have yesterday ‘decommissioned’ the one remaining Gen1, it is unplugged and no longer part of the system.

When I now login tot sonos site, it only shows an old Gen1 (now no longer in use) and the two brand new series 5. The two upgraded series 5 (gen2) no longer show up in my inventory….

Hi. I think it would help if we used standard terminology. There is no Series 5. The speakers are called:

Play:5 gen 1

Play:5 gen 2

Sonos Five 

Could you have another go at explaining what you have please?

Apologies:

• 2x brand new Fives: bought using the upgrade offer
• 2x Play:5s (gen 2): opted to úpgrade these, expecting to continue to use them
• 1x Play:5 (gen 1): no longer used, unplugged
• upgraded the system to S2 yesterday
• (also own 2x play1, that both work with S2 and show in my rooms list: no issues)
• Sonos S2 app: rooms show two brand new Fives, and 2x play1, but not the two Play:5s gen2 that I already owned.

Moderator Edit: Edited for technical correctness, just to get things moving in the right direction.

• but not the two Fives gen2 that I already owned.

Those must be the Play 5 (Gen 2)'s, that are indeed both S1 and S2 capable. Are you sure they have updated to S2? Are they visisble in the S1 app if you would install that?

If the Play 5's are indeed still visible in the S1 app, I would need to check. (not at home right now). I will verify tonight. 

If indeed visible in S1 (which was the status two days ago), adding the Play 5's to the S2 should also update them to S2 right? Or should I do that from within the S1 app?
 

The steps to update S1 speakers to S2 are mentioned here: https://support.sonos.com/s/sonos-s2-overview?language=en_US

If the Play:5/gen2 are visible in the S1 app then the speakers are connected to the wrong/old system.

1. Uninstall the S1 app. You won’t need it any more, and it could confuse things. 
2. Factory reset the Play:5s.
3. Go into the S2 app and add them. They will update themselves to the correct firmware automatically.

I suspect the problem has arisen from one or both of the following:

1. The way in which you transitioned from S1 to S2 - @106rallye ‘s conjecture being a very plausible example of this
2. Not factory resetting the Play:5 gen 2’s correctly

I am surprised the Play:5 gen 2s have disappeared from your Sonos account, as this would normally only happen if they were added to a different Sonos account…. but let’s park that thought for the moment.  We need to know whether the Play:5 gen 2s are still in your S1 system.

Edit: You mention that you reset the Play:5 gen 2s.  You don’t actually say that you have re-added them to the system using ‘Add Product’, or at least tried to.  Did you do so?  If so what happened?

That appears to be where the OP is stuck as they originally stated:

Tried factory resets (after which they are visible to the app, but warning appears: 'they may not show up in your system, just unplug and plug back in', but never actually show up in my system. 
 

Maybe try connecting the Play:5 to your router by Ethernet whilst you attempt to add them to your S2 system.