I’ve got a problem that KiCAD rplaces my Reference J100 with #J046 when executing an ERC or export to the netlist. I do not know what the problem is, nor how it can be resolved.
As Davidsrsb suggested, you can try directly editing your schematic (and/or project-cache.lib) in a text editor.
It also seems to be a custom symbol.
What happens if you remove it and replace it with (a different) default library symbol?
After a schematic is saved Kicad 4.0.7 (4.0.5 probably also) puts copies of the used default library symbols in the project-cache.lib file.
You can compare the text of your symbol with one from the default libraries, and look for the differences.
File formats of KiCad’s files are documented on the KiCad website.