Another possibility is ...

Another possibility is chlorine damage to the RO membranes.  Chlorine damage will initially result in a reduction in flux, followed by an increase in both flux and TDS concentrations in the permeate.  So, an apparent increase in flux could be a failed seal or failed membrane.  Comparing the current flux rate with your previous flux rate won't help clarify the problem as both result in similar outcomes (increased flux and TDS).  Get your equipment supplier to help with troubleshooting the problem.