Upvote:0
Tour operator normally could not cancel a visa (and not for Schengen), but they may withdraw some guarantees, so the visa could become useless.
Visa could also not be valid (but this is different from cancelled), if circumstances changed in a significant way. This may be the case of some tour operators, but it is for very special cases (specific tour with specific circumstances [I would say organized, but not touristic], for specific people [e.g. students visiting UN or medical organization coming from few particular countries where visa were seldom given)
We do not have all information, but if you do a touristic visit not very dissimilar to original one, it is not a problem. Also for this reason (I think), they will not refund the visa costs: you can still use it.
Upvote:2
Once the valid visa is issued by the embassy, I highly doubt it can be cancelled by a local tours and travel company. They would need to fill in additional paperwork to cancel the visa. Also since they are not refunding the visa fees, its proof that they dont expect you to travel with them in spite of having a valid visa. I think you should not worry about it.