The increasing use of embedded systems to provide new functionality and customer experience requires developing the embedded systems carefully. As a new challenge, autonomous systems are developed to be working in a fleet to provide production workflows. Developing such a system-of-systems requires utilizing various software tools to manage the complexity. One task in developing safety-critical products, in general, is to analyze if the applied tools can introduce failures into the final product. Today's functional safety standards consider only single software tools for analysis. In our industrial work, we can observe a trend towards supporting product lines. A common configurable platform is developed to support a range of different products. Developing such a platform and supporting variability, a toolchain is created where software tools are glued together using scripts to support product lines and automatically generate compiled code. The current functional safety standards do not straight forward support this. This paper discusses how software tools need to support functional safety and show limitations by providing an industrial case. We provide a model-based approach to describe a toolchain and show its application to an industrial case. To analyze potential failures in the toolchain, we utilize the HAZOP method and show its application.