There isn't an easy answer to this question. In the case of cells labelled through introduction of a GFP gene into the DNA of the host cell in a whole organism context such as transplantation, then a lot depends on the promoter being used. Promoter silencing may take place but with correct promoter choice is not inevitable. GFP is associated with slight toxicity in some cell types and situations, and may also be immunogenic although this varies with the host. But nonetheless it has been used to look at cell fate in a variety of developmental and transplantation models, some of which are fairly long term. One possibility to minimise long term loss of GFP reporting in a transplantation model might be to consider an inducible system.