When a improvement is destroyed and only 1 can be built on the planet; the option to rebuild that improvment is gone.

This could happen either of 2 ways - (1) invading the planet: planet invasion w/ using tidal invasion or mini-soldiers. (2) re-laying out the planet, e.g. AI built the quantum factory on a tile u wish to use, so you decommission the improvement. In either case u are unable to rebuild the improvement.