You have (most probably) created some new items/scenery/critters/etc, and placed them on your map. The information of these new additions were stored in your "../fallout2/data/protos/" directory. This directory (and all of its sub-dirs and files) should be set to "read-only" once you're finished creating new protos in FO2Mapper.
Because... When the game is started, it's gonna erase all new protos promptly. This means all info about new stuff you have made (and put in your map) is permanently lost and there's no way to bring it back.
Next time watch for it. Make backups of your proto dir often, also of your maps. Make more experiments before creating something serious (play with the Mapper for a while).