If the system is missing from the ePO system tree and there is no apparent cause (nobody deleted the system, there is not a task to delete\cleanup systems, etc.), then the next item to suspect may be the situation within https://kc.mcafee.com/corporate/index?page=content&id=KB52949. It would definitely be worth looking into.
To gain access to the system, if you are not able to log in with any user and the challenge\response recovery options are failing, then you will most likely need to utilize DETech standalone to first pull the disk information which should contain the keycheck value. You should be able to use that value to obtain the recovery XML since the system entry isn't there. Once you have that, you would want to confirm that the XML file is correct in DETech and then complete an emergency boot to get it.
If you are having the issue in KB52949, the potential for the issue to continue happening exists, so I would recommend looking into that as soon as poss