All the backerboard and existing thinset needs to be taken off. Otherwise, it's a contaminated substrate and the new backerboard may not properly adhere. Backerboard can usually be taken out using a circular saw. You need a carbide tipped blade. The more cuts you may the better so that the...
This could be related to using an incorrect amount of water when mixing the grout. Adding more water may make grout easier to apply shortterm, but it can have negative affects on the installation afterward. That's why it's so important to follow the grout manufacturer mixing and application...
You can install a vaper retarder membrane behind cement backerboard to prevent mold and mildew. Then tape the seams over the cement backerboard with alkali resistant tape. And patch the seams with skimcoat and patch.