If a definition file is read into CFX-Pre and then re-written, then convergence behaviour can be different even if nothing was changed that ought to affect convergence.
CFX-Pre is not consistent about what order it writes the region data into the definition file. If this order changes, then the solver may solve things in a slightly different order which can affect convergence (although not the converged solution). This is only likely to be a significant effect when the convergence of the case is particularly sensitive.
In some cases it may be possible to avoid rewriting the definition file i.e. by editing the command file directly instead of using CFX-Pre to re-write the whole definition file.
ANSYS CFX 11.0 Update 1.