Provided that a 'Release Agent' is used on all the surfaces that the glass bedding material will come into contact with are correctly coated, there shouldn't be a problem. Sadly many people don't bother to do this job correctly and the woodwork and metal are well and truly stuck together. Contact the maker of whatever glass bedding kit you want to use, and ask their advice on what release agent works best with their product.
Glass Bedding is often carried out before a firearm is customised/ restocked/ blued or browned so there is no harm in taking it apart after the bedding material has set simply to see if it will come apart. If won't, then your stuck with it like that until you whittle all the wood away and start again.
Harry