Thanks so much for the detailed write-up, this is really helpful context. 
A few things here:
On the slowness: This is something we're aware of and actively working on. Assist loads your entire app into its context window, so the larger and more complex the app, the slower and less consistent it can be. For now, breaking tasks into smaller, more targeted prompts tends to help. Here is a similar suggestion I gave in another thread.
On the corrupted layout with the collapsible containers: This is something we've seen reported before and are looking into. It's possible that Assist's handling of layout positioning in complex nested setups like this can sometimes lead to unexpected results. For now, the safest workaround is to handle layout changes on nested containers manually rather than through Assist.
The .rsx file stands for Retool Scripting XML, part of Retool's internal framework called ToolScript. It's not directly editable by builders. Since it's proprietary to Retool, it isn't well understood enough by LLMs to be reliably authored or modified yet. It's something the team is actively working to improve.
On the delete/recreate pattern: Totally valid frustration! Complex reorganization tasks can still be hit or miss, it's something the team continues to work on.
Again, thanks so much for the feedback, really appreciate you sharing it! Assist is still in beta, so we're actively iterating and input like yours goes a long way. I'll make sure to pass this along to the team. 
In the meantime, check out our latest announcement on recent Assist updates. There might be some improvements there that are relevant to what you ran into!