as long as it is going between equipment (and the equipment is set up for it), it should be fine. It is the direct connections via patch panels that wouldn't well, if at all. check the specs on the equipment if you can to see what it will take, and put out. in most of these situations that i've ever seen, they had a fiber switch to take a WAN or trunk sm, and multiple mm legs for LAN distribution.
the 50 mic is there as they added on to an existing backbone, or a contractor just got cheap. hopefully your jumpers are labeled, because that might give you some problems: 62.5 patch panel to 50 jumper and vice versa.
the unmarked cables, well, good luck. sometimes manufactures put the fiber type on the connectors, so you may want to check in the panel. if they have any markings at all, or color for interior, put it on here. i may have seen it before. they are probably older though, cuz they almost always put everything on the outside of newer cables.
hope this helps. fiber can get tricky.