Next time she is planning on being off I would ask her to give you a list of the things she wants you to do. Then keep an 'hours' diary of what you have done as you may be asked to do 'other things' by your other boss and she will then be able to see how you have spent your day. It is not your fault that the lines of communication regarding work allocation are not as they should be between your 2 bosses.
I have two immediate bosses, boss one is lovely we get on great together and work well as a team, boss two not so much, I went into work as normal, and before I had properly got started, turned on pc etc, boss 2 turned on me, almost shouting that we as in boss one and I had no work done while she was off for few days, she kept on and on, I tried defending myself and boss one who wasn't in, We had done a lot of work, but obviously not what boss 2 had expected to be done otherwise she wouldn't have gone off on one, After her tea she came back and appologised for being cross, but that doesnt mean much really, she didnt appologise for stopping short of accusing me of twidling my thumbs for the week, did she mean what she said, or was she appologising for her tone, or really. Was she shouting at me for boss 1 not doing all that boss 2 expected even though I wasn't asked to cover any of the specific tasks in question for boss 2, by either if them, I feel now really uneasy, should I leave it, should I bring it up with either boss? Upper management, I have never contracted hr before, I was thinking of diarying all the elements of a task, ie check x, spotted problem, rang y, emailed z by 3, prosess, record, copy, file, basically record every tiny thing I do so that if she comes back I can go well since I wasn't trusted to work under boss 1 supervision, here is what I do all day, what annoyed me even more was that she thanked me for doing a great job when she was leaving, I am confused, annoyed, and anxious, So after reading that rant essay, WWYD