There are a number of ways you could approach this...
For starters if you use an off-line workflow you can have far more than 1000 features, . We've done data collection using runtime apps that generated upwards of 500k features sync'd them across multiple devices and it worked.
If I were in your position I think I'd consider one of two options:
- Create a non-editable building footprint layer for display purposes, then add a second "survey buildings" layer in which you drop the current batch of buildings to be surveyed.
- Add a related table to your database, and use that to collect whatever data is included in the survey.
Either way keep in mind that you will eventually end up with some pretty large archives/business tables in your SQL Server database. We've frequently run into issues where that archive becomes corrupt, or ArcGIS Server/AGOL runs into other issues when syncing the data. The only option is to then clear and re-build the archive, republish the service, and in the case of collector remove and re-download the map to your devices.