As far As I understand your question " you need to clean FTO slides with HCL".
The effects of HCL on FTO or ITO coated glass substrates are varied. Once you clean the FTO with HCL it may damage the FTO layer and brownish color will appear on the surface. Usually, HCL with Zn powder were used to etch the FTO coated glass from one edge of the substrate to avoid the short circuit in case if solar cells or any other devices.
To remove ZnO films from the conducting glass FTO substrate, try to dip the film in KOH solution in water. Take a 100 ml beaker, put some fresh KOH pellets (6 to 8) into it, and keep the beaker on a hot plate and heat upto 150 deg c. See if it can selectively remove ZnO and retain the FTO coating. Don't use HCL.
Yes, It will affect the conductivity of the FTO, remember acid will attack the metal (corrosion) and oxidise it, however it depends on the concentration of acid you are using, it is like etching of the FTO surface, if you leave it for long time in HCL you are gradually removing the FTO layer, in other word you are reducing the thickness and at the same time oxidise it, then the resistivity will change