You're probably right about the eMMC.Reflowing was unnecessary in your case. General assumption for breaking CLK is digging too deep into the blind via resulting in cutting the connection.
Question about that via. Is that trace coming from the SoC, going through the via to the underside of the board and connecting to the eMMC somewhere? If so, then why so we not pick up the signal on a track on the underside of the board? It seems quite challenging getting it from the via near the SoC.