You should be using the sencha touch 2.2 proxy if you're on 2.2 now as that works fine for me. It filters using queries on the database with the filters param rather than remoteFilters but this works just fine.

I would recommend people switch over.

As for persistancy, please be aware that sqlite and websql are different things. They happen to share, for the most part, their query language, but here is the main difference:
- websql is a browser based database implementation. Sometimes it works on a sqlite backend. The W3C have abandoned the specification for this since 2010, but it remains implemented in nearly all modern browsers. IT IS NOT TRULY PERSISTENT! Any user can delete the data from the browser at any time they wish.
- sqlite is a type of database that can be accessed on most platforms, and relevantly here iOS and Android. It is NOT websql, although websql may be working with a sqlite implementation. Sqlite itself is therefore only available through natively packaged apps, and you'll need something other than HTML and Javascript to implement it. I believe Sencha has implemented such a feature in 2.2 and there are cordova plugins available. If you use these, then the application that has control of the database is your app - not the browser. You can control where the sqlite file goes, therefore controlling its persistency (make sure you put it in the relevant place on iOS - this is determined by whether the data is user generated (needs to go in icloud folder) or data that could be redownloaded again from your servers).