I remember removing roughly 10,000 tweets once using a similar tool and it broke Twitter for me. Every time I tweeted, it didn't appear in my timeline. Oddly an old tweet from a previous account (with the same handle as mine) showed up too, as if I owned it, but I didn't; I merely reclaimed the handle.
Deleted like 3,200 and worked fine for me
Is that really enough for Twitter to remove the tweets from their databases?...