Induction of post-transcriptional gene silencing (PTGS) by transgenes can be exploited in the genetic engineering of plants for virus resistance, altered lipid or polysaccharide composition, delayed flowering, reduced toxin or allergen content, and many other desired traits. Transformation with constructs based on virus coat protein (CP) genes or other viral genes has been successfully used to engineer PTGS-mediated virus resistance into a large number of crop plants and some transgenic lines have been commercially exploited. However the discovery that plant viruses encode suppressors of gene silencing has raised concerns that virus infection of crop plants might reverse the new silencing-based traits. Most studies of virus suppression of silencing have used model systems based on silencing of reporter genes. A few studies have analysed the effects of virus infections on plants with genetically engineered virus resistance based on either a simple sense or an inverted repeat construct. We decided to use genetically engineered virus resistance in potato as a model system for further studies of the effect of virus infection on genetically engineered traits. We present for the first time a comparison of simple and inverted repeat constructs with respect to resistance stability upon challenge with another virus. We found that silencing induced by an inverted repeat construct persisted after virus infection where silencing induced by a simple sense construct failed. Furthermore, even with a simple sense construct the virus-induced suppression of silencing was partial and transient, suggesting that silencing based traits can be agronomically highly useful.