Defender emoberlizer problem

Hi I have just cut out and replaced rusty rear quarter on my defender 110 td5 county. Also refitting fuel tank and loom. After reconnecting battery I switched on, engine turned over but in a split second I realised I hadn't replaced fuel . So did that and purged. Then tried to start, but emoberlizer kicked in!! Put in code but nothing, tried a couple more nothing. Now my question is can the battery which reads 11.98
have anything to do with the emoberlizer code not working? I have now removed battery, but would you credit it charger wasted! The battery has been out for 6hrs so I have just checked it again and it reads 12.3. Ps fob batteries seem fine. Any help would be most appreciated cheers.