Fairly certain it’s a limit of the API; this happens in Kraken too.
It would be nice if the clip limit was removed, though, and it would solve your problem completely.
Unless they remove the limit, you might have better results using Kraken for this bot.
Helix’s clip discovery uses the window of time “all” aka, the top most viewed clips for a channel, up to 1100 clips like you said.
You can use Kraken to search for 1100 results of “all”, “month”, “week”, and “day”, which gives you up to 4400 clips (but more realistically ~2000, and there will be duplicates)
This doesn’t solve the problem, though; there will still be missing clips (for example, stuff with few views from a year ago).
Still, might be your best bet for the time being!
I’m personally hoping that they will let us set the window of time with Helix’s clip discovery in the future. “week” is incredibly useful for streamers looking for their own recent clips.