OK so i have asus rog rampage vi apex mobo with an asus 2080ti oc in 1st slot and evga 2080tiftw3 in 3rd slot and a asus hyper m.2x16 nvme card in 2nd slot and my board configured 1st slot gpu at x16 and 3rd slot gpu at x8 and both cards in sli using evga 3 slot nvlink but in nvidia controller panel the card far away from gpu which is evga is displayed as number 1 and the asus gpu that is closest to cpu is displayed 2nd and i have few issues, whenever i disable or enable sli through nv control panel i loose video signal, it works sometimes and doesnt work some times and after further closer look at the nvlink hardware it says cl1 and cl2 next to the x16 pins and cl2 is connected to 1st gpu and cl1 is connected to 2nd gpu and i am not sure if the nvlink itself is causing this issue, i am aware this is 2 way nvlink but i strongly suspect it is making the nvidia control panel read the card order incorrectly and on top of that one of the cards is always stuck at 300mhz gpu clock and memory clock stuck at 405mhz as if the gpu driver has crashed and uninstalling gpu drivers using DDU in safe mode fixes the issue on some occassion but it appears again, is there a solution for this. BTW both the cards BIOS are stock and unmodified, any help appreciated.

thanks @bcavnaugh, so another issue, in evga x1 the cards are displayed correctly as to which is 1 and 2 but in hwmonitor64 they are displayed incorrectly and the evga card is constantly stuck at 300mhz/405mhz all the time whether sli enabled or disabled and it is running at x8 speed and it is detected as the primary card even though its in 3rd slot and i believe its the nvlink telling nvidia control panel about the order, both cards used to display good speeds but in the last week evga is constantly stuck at 300mhz gpuclock/405mhz mem clock and it worries me, i have updated the bios from the techpowerup just now and clean installed drivers again just to make sure but still the same case, i have read its normal for card to be at 300mhz but i believe it happens when gpu driver crashes or something else, how do narrow down the issue.

The GPU order being wrong is common. It's been this way for years.

Windows and the NVIDIA driver doesn't store a record of the GPUs in any particular order. Most software incorrectly assumes that the first one in the list is GPU 1 and the second is GPU 2 and so forth, when in actuality that may not be the case. There is a method software could use to verify which GPU is actually primary and which is actually secondary or tertiary and so forth, but most programs don't bother. So, until NVIDIA fixes the issue in their NVAPI or software programmers start to care, this will be a normal occurence.

There is a software developer who enlightened us about this a couple years ago, gave us some examples, and told EVGA how the issue could be rectified in Precision software, but EVGA has not listened. It honestly doesn't matter too much if the EVGA Precision development team fixes the issue in Precision, since all the other software will still be wrong until they also care enough to fix the issue. Ultimately, it would be nice if NVIDIA fixed the issue in NVAPI to solve the issue at the root.

@bcavnaugh if i connect my monitor to 2nd gpu while in sli there is no signal to monitor, only from 1st gpu my monitor gets a signal, i have tried running superposition benchmark with sli enabled and in the top right corner where the data is displayed only the 1st gpu shows up and 2nd gpu is not shown running, now regarding the gpu placement since the evga has better stock boost clock than asus gpu should i move ftw3 to 1st slot so i get better performance, another question is since both gpu act as masters in nvlink rather than master and slave in older models how is this work shared between the gpu in sli. And since i have 7900x cpu with 2 gpu attached and an asus hyper m.2 x16 expansion card for cpu data for improved speeds my mobo only configures second gpu at x8 even though i have many pcie lanes left not used, how can i force it to be at x16 without removing m.2 expansion card.

What ^ Said.