Catholics should remember that Jesus is there, whether it is in a monstrance (covered or not) or in the tabernacle. There are exceptions, but the rule is that when the Blessed Sacrament is present, there is supposed to be a vigil candle burning.
Theologically, Jesus is there. There is no reason to doubt.
Another generality is, that the Eucharist is usually not exposed unless THERE IS somebody there, like a volunteer who has signed up for adoration. The fact that you were alone, is an indication of something – maybe the door should have been locked to the chapel, to begin with – not leaving the Eucharist unattended.
The more I think about it, maybe the monstrance was covered because the Eucharist was not in it, and was safely stored in the tabernacle. There are practical rules, and it is hard to say how they might be interpreted in each case.