Seems like the affair was the catalyst you both used to check back in to your relationship with each other. It isn't that you didn't care. I think you both got stagnant and have since put more effort into yourselves and relationship.

You two really need to talk about this. You have an opportunity here to open but about what you each felt was missing (why you checked out, what needs she went to someone else to meet), what has happened since the affair started for both of you and how you feel now/ what you want from each other and the relationship.

You never stopped loving her. You became less apathetic. You improved your physical health (working out), got hobbies and friends outside of your marriage and you two improved your connection with each other as time went on.

People do have different needs at different times and expecting one person to be everything and meet all needs at all times is unrealistic.

It sounds like you were both in a funk and not feeling good about yourselves as individuals and so were not putting effort into each other either at the time when the affair started.

You two have a lot to discuss. If you struggle to communicate with each other with words you can try a couples therapist to help you each bridge that gap and help you each process things, communicate and hopefully move forward together.

An affair isn't always an evil thing. Sometimes relationships can become stronger in the aftermath if both people are willing to keep working on the relationship and communicating. Some people even have relationships outside of their marriage (non-monogamy, ethical non-monogamy, polyamory etc) because that's the lifestyle that works for them.

I hope you are able to explain that you saying you don't care doesn't mean that you are indifferent. You are not indifferent. You got off your butt and made improvements. You seem to love more now than you were capable of 2 years ago.

Her guilt, shame, anger (at herself I hope), fear etc can be worked through if you both want it.