We can make some very good analytical revelations here:
First York mentiones that the timeline is messed up and she cannot come up with why Vegapunk knew the mother flame had been partly stolen and was being used on Lulusia. In other words: If the Stellar had known of Lulusia being destroyed with the help of the mother-flame, York would have known too. But the Stellar showed genuine surprise that York was a traitor - so he did not know of her betrayal. This means that at the time of York’s revelation of being the traitor, Vegapunk had not known that the mother-flame was used on Lulusia and that York had stolen it (Note: Oda left it also open, when Vegapunk came to know that part of the flame was stolen. In his message the Stellar did not specify when he noticed it missing.). This means he must have found out about the mother flame being used on Lulusia during the time-skip.
Which brings me to the next little thing, that we now have to look at:
In his recorded message to the world however, the Stellar apologizes for being part in the destruction of Lulusia. Since he did not know that the mother flame was used to destroay Lulusia beforehand, and learned about it during the time-skip, Vegapunk must have also recorded the message during the time-skip. Otherwise he would not have apologized to the world for his involvement in that sad incident. This means that Shaka and Phytagoras are still alive, as we see them recording the message with the Stellar.
What is strange however is the fact that Vegapunk in his recorded message is missing the band aid on his forehead, which he had, when the time-skip had ended and we saw him with the whole crew again in chapter 1089.
Either this is a mistake by Oda or the Stellar did record the message earlier, but didn’t tell York. In this case it is questionable, if Vegapunk knew that there was someone in his near vicinity, who was betraying him and therefore did not share all information with all his Satellites. Who the Stellar knew he was able to trust is another question, we would need to have an answer for - in that case.
But in case option number one is correct:
We still have the fact that the snail is with the giant robot. Interesting is that the robot is in the Fabrio-phase, not in the Labo-phase. This is important, since we have to consider something very strange:
Stellar was not aware of York being a traitor. So, until she revealed herself as being one, Vegapunk shared everything with her through sychronisation of their thoughts/brains. If Vegapunk had hidden the transponder snail within the giant before this revelation, York would have already known, where it was. This was not the case, so the snail must have been hidden after York was revealed to be a traitor - and therefore deemed untrustworthy. This means that during the time, the snail was hidden, the barrier was either up and locked with York’s code-word – in this case someone in the Fabrio-phase could have helped with putting it with the giant. But this begs the question, how the snail or information could have come through the barrier to reach this someone?
Or the snail could have been hidden with the robot after the barrier had come down. In this case, we need to know, who it was, who hid it with the giant, because everyone Oda depicted had not done so. This means that an unknown party did hide the snail. And we know that an undefined party was already giving Luffy food.