How do I handle an inappropriate colleague and move on?

My immediate response here is that your more senior work colleague was completely in the wrong. For whatever reason, she has ultimately used her more powerful position unwisely and created an environment where you have felt trapped and unable to discuss what was happening with either your HR department of with your own partner. I understand that you thought it just some harmless flirting and that you and your partner generally feel ok about flirting with other people, however, it sounds like you and your boss had different interpretations of where things might go when the flirting stopped. 

As a newbie, a boss  or senior work colleague has the responsibility to provide a safe and supportive working environment. It sounds like her attempts to create something more personal and quite frankly controlling would be likely to worry and confuse a new employee in equal measure. My suggestion would be that should she make any further inappropriate moves towards you that you speak directly with a different senior colleague or with HR.

The bigger problem now is the guilt you feel about not telling your partner what happened. I'm also wondering whether you have secret concern that at some point your boss might make some 'casual' comment about the two of you enjoying 'something special', even though you  rejected your boss's inappropriate advances at every turn. I wouldn't be a bit surprised if your boss knows that might be a worry of yours and rather enjoys it.

You tell me that just getting a work related email  from her reminds you of all the difficult stuff. I'm wondering if you were able to resolve the conundrum of whether to tell your partner what happened, the impact of receiving an email might lessen. Only you can decide if telling her would be the right way forward but sometimes, having things out in the open means that the secret, what ever it might be, loses it's power to maintain any hold over those involved. 

So, to conclude, a word to the wise. Flirting is fun and usually harmless, but only in the right context. In the one you describe, whilst I would say that this woman is at fault overall, you perhaps might have yourself wondered about the potential issues arising from flirting with a senior colleague  in a company that was new to you. Sometimes such a casual approach to flirting is just not a good idea as you have learned to your cost. Perhaps a golden nugget to store away for future reference?