Sorry for the late reply.. I have exported these now and will send them once it changes again so you have before and after.
Just to clarify my "external" drives are connected via a sata hot swap bay so they appear to the system as internal drives. This explain why adding and removing them messes with the list. This is not really a problem though.
What seems to be the issue is that the drive numbers associated with a particular drive changes on reboot (not all reboots I don't think). So one drive was set to "data\sensor\aida64\thdd32_0" in aquasuite but after reboot it changed to "data\sensor\aida64\thdd24_0" and requires manually updating in aquasuite.
If I look at my current log file it looks like this for the drives
HDD10,°C,19,17/05/2017,18:27:25,36,18/06/2017,19:56:29,28.5
HDD11,°C,37,19/06/2017,20:11:32,37,19/06/2017,20:11:32,37.0
HDD15,°C,37,19/06/2017,20:11:32,37,19/06/2017,20:11:32,37.0
HDD20,°C,18,18/05/2017,17:12:42,41,21/05/2017,19:25:47,30.2
HDD21,°C,19,17/05/2017,18:26:53,38,26/05/2017,23:23:37,32.6
HDD22,°C,19,17/05/2017,18:26:53,37,27/05/2017,13:55:50,31.0
HDD23,°C,17,18/05/2017,17:12:42,38,14/06/2017,19:25:24,32.8
HDD24,°C,19,17/05/2017,18:26:53,40,19/06/2017,20:03:53,31.1
HDD25,°C,20,16/05/2017,17:37:33,40,19/06/2017,20:14:10,32.6
HDD26,°C,18,05/06/2017,17:55:11,37,25/05/2017,22:03:23,30.3
HDD27,°C,18,17/05/2017,18:26:53,35,26/05/2017,23:56:49,30.6
HDD28,°C,18,17/05/2017,18:26:53,36,23/05/2017,18:51:26,29.7
HDD29,°C,19,17/05/2017,18:26:53,37,19/06/2017,19:51:07,31.4
HDD30,°C,18,18/05/2017,17:12:42,39,26/05/2017,23:48:51,33.6
HDD31,°C,18,17/05/2017,18:26:53,37,21/05/2017,19:25:16,29.9
HDD32,°C,19,17/05/2017,18:26:53,39,26/05/2017,23:56:49,33.1
HDD33,°C,19,17/05/2017,18:26:53,38,14/06/2017,19:23:18,33.1
HDD34,°C,18,17/05/2017,18:26:53,38,19/06/2017,20:14:10,30.2
HDD35,°C,18,18/05/2017,17:12:42,40,19/06/2017,20:08:43,30.3
HDD36,°C,19,18/05/2017,17:12:42,38,19/06/2017,19:59:07,30.8
HDD37,°C,19,17/05/2017,18:26:53,35,07/06/2017,13:16:46,25.2
HDD38,°C,19,16/05/2017,17:37:33,35,26/05/2017,23:24:40,28.3
As you can see the number range massively and some are missing etc.. Is there any way on the startup of aida64 the drives could be ordered corresponding to system drive number and then assigned a number? I don't really understand why numbers are missing (e.g. HDD12)
EDIT: No drives were added or removed at all from startup so that could not explain missing numbers