According to a recent podcast by the folks over at www.batman-on-film.com, Affleck's Batman will definitely shoot in Los Angeles. The sources are quite adamant in this, stating that the majority may film at Warner Brothers' Burbank studio. It may not be all sets, as there may be need for some out-door filming for various scenes according to the script.
WB has not yet confirmed or denied this particular filming location. Justice League recently finished filming in London and Iceland and Aquaman is set to shoot in Australia and other locations around the world. The script has still not yet been finalized, so definitive location shoots are still not settled upon but most importantly, according to Affleck, is that the script is good. If it doesn't come up to par, the Dawn of Justice and Accountant star will simply "walk away".
The Batman is set to hit theatres sometime in 2018.