Hi Miguel,
Firstly, now you've bought a Moody, it's time to sign up to the MOA - the annual fee of £22 is peanuts for the money you can save with advice from here. Whatever problem you find, you can e sure someone has found the same before you.
I'm not completely familiar with the M46 but, as far as I recall, she doesn't have a baby stay - that is an alternative to the forward lowers, joining the mast at the same height as the aft lowers (around the lower spreaders) and too close to the mast to be practical to set a sail on. Most M46's I recall are cutter rigged, so they have a cutter stay (or inner forestay) which joins the mast at about he height of the upper spreaders and is normally associated with running backstays to balance the loads. The inner forestay usually tacks down nearer the stemhead than the mast.
Firstly, with a staysail set on the cutter stay, it is not usual to set a full genoa on the forestay, but a yankee which is less than 1.5J wide and has the clew cut much higher. A Yankee should be no harder to tack through the slot than a 150% genoa is to get across ahead of forward lowers on a sloop. If yours is fouling on the way across, it might be worth looking into what is causing the problem - a smooth knot to join the yankee sheets to the clew can make a difference. I'm also starting to wonder if your boat has come with a big genoa, as she would be undercanvassed sailing with just yankee and main.
So, in my view, rigging and then unrigging a cutter stay is unlikely to be unsafe, but I would check with a rigger before making that change. However, rather than doing that, I would have a think about whether you want to sail her as a cutter or as a sloop then, if you prefer a sloop make the change permanent. If she becomes permanently a sloop, you could do away with the inner forestay, the running backstays and the staysail halyard and sheet - a simpler rig, if that's what you want. Otherwise, stick with the cutter rig - it has real advantages when you have to shorten sail .
Hopefully someone who has sailed a M45 will be along to advise you soon.
Peter.