How long is too long on fruit?

Depends on what you're going for. What you described doesn't sound like too long at all, considering some people leave beers on fruit for 6 months. If you properly sanitized the fruit, then you're definitely fine at 3 weeks on the fruit.

 

I would like to think that the frozen fruit is probably okay, but I don't have any experience using frozen fruit. Sorry.

 

FWIW, freezing does not ‘kill’ microbes:

“Freezing to 0 °F (-17.8 °C) inactivates any microbes -- bacteria, yeasts and molds - - present in food. Once thawed, however, these microbes can again become active, multiplying under the right conditions.”

Cheers!

 

Ive done 6 months on fresh fruit the only issue is after about 3 the fruit really starts to break down and can clog your system during racking/bottling etc

 

I've had great luck racking into a vessel that has a sanitized paint straining bag around it. Instead of trying to wrap my racking cane or use a sack that I have to fish out of primary, I'll just wrap the secondary and pull the pulp that I can. I do this for wine, and I just did this for the first time for an APA.

 

The sugars in the fruit are more than likely fermenting out, which is why there's still activity.

When I fruit a beer that I want to drink fresh like you're doing, I do it in a keg and immediately put it in the kegerator to minimize refermenting.

Watermelon and habanero pepper is a great combination in a wit!