You have two of the best giving you advice. Both AS and sandi are huge helps to LBSs, this guy included.
Here is what I would suggest:
First, she is definitely taking steps towards moving back to the MR. The question is, why? Did the AP end things or start giving her the cold shoulder? Is she suddenly afraid of that her life will become if her PA is made public and the result it will have on her current situation (IE she is trying to throw you off the scent)? Does she have a vested financial interest in holding things together with you while she is off screwing another guy? Likely you do not know her motivations. But it could be any number of things.
So like AS said, you have to keep giving her space.
Now, as too affection. One of the things we try to stress to LBSs is that you shouldn't be cold, indifferent, or mean in a passive-aggressive way. This means that flatly refusing her shows of affection without her knowing why is probably not going to go over well. Normally we tell LBSs that it is okay to say ILY2 if she says ILY first. Or it is okay to kiss her back if she kisses you. Or to hold her hand if she initiates. Or even to have sex if she initiates sex. BUT NOT IF THERE IS A PA.
WWs as sandi says needs tough love. Even in the absence of a PA. When there is a PA involve the rules have to change. You should be avoiding her affection at all costs. You certainly should not be having sex until she has been tested for STDs and you know without any doubt that the affair is over.
So how to proceed? Well first you have to move her out of the MBR. You should not be sharing your bed with a cheater. Personally, I would confront her simply by tonight, when she goes to get into bed, letting her know she is not welcome there. When she protests, complains, gets upset, etc.....calmly but firmly tell her "I know what has been going on." And then end the conversation. Do not tell her what you know, or how you know, only that you know. Even if she presses you for details, you simply tell her "I know."
That will be the real test of whether her PA is over. She'll either be defiant (it is still going on), or she will break down, admit to everything and be extremely remorseful. Likely it is over, but again, you have to be sure.
So when can you be sure it is over and that she wants to commit back to the marriage? When her behavior is consistent over a long period of time. When she is willing to agree to any and all requirements for reconciliation (writing and sending a cease and desist letter to the AP with your full knowledge of what it says and that she sends it, full transparency (which means no unknown passwords or accounts, I'd even suggest getting a phone app like Life360 so you both know where the other is at all times, she gets herself into a pro-marriage IC on a weekly basis, and once you feel comfortable a pro-marriage MC for you both to see).
As AS says, keep DBing. As sandi says, you need to confront her but again play your cards close to your vest. All she needs to know is that you know, not what you know or how you know. And I certainly would not allow a cheater to share my bed with me at least until I was sure that the PA was completely and utterly and irrevocably over!
M(53), W(54),D(19) M-23, T-25 Bomb Drop - Dec.23, 2017 Ring and Piecing since March 2018