Hi Kris,
can you tell us which exact Matlab Release you are using? I had similar problems with R2017a/b, but R2018b runs quite well for me now (I have also some apps with around 1000 lines).
Anyway, if possible, it is always good to keep your code below 1000 lines since App Designer has some known issues (I have read an article about that from Mathworks but can't find it now). Disabling the "app coding alerts" (Editor > View) can extend this to 1500 lines, but that is not a solution in debug mode.