I have a theory on why the Gorosei ordered Vegapunk to erase Kuma’s personality. It was because Kuma was trying to awaken Luffy (Nika).
We know from Chapter 1095 that Kuma strongly believes in Nika. We now also know he was in God Valley.
From the many chests in God Valley, I think it’s highly possible that the Gomu Gomu no Mi was inside one of those chests during the God Valley incident.
I think somehow, Kuma learned the truth of the Gomu Gomu no Mi. This is why he was protecting Luffy in Saboady, and why he protected the Thousand Sunny during the timeskip. His plan was to protect Luffy and help him awaken.
The Gorosei realized this and they decided they need to stop him, to prevent the return of Joy Boy. However, Kuma was too useful to them with all the experiments Vegapunk was doing on him. Their solution was to order Vegapunk to erase his personality.
*by PM_ME_UR_SO