The Senate can't remove the pre-existing conditions protections or letting young adults stay on their parents plans through budget reconciliation.
They can remove funding for subsidies through budget reconciliation, and let the system collapse on its own, but they don't have the votes to overcome the filibusterer they'd get if they tried to remove those protections directly.
1 of 2 things will likely happen.
1. They will repeal and delay. Meaning they will remove funding through reconciliation, but delay implementation until 2020. Then depending on what happens in 2018 who knows what might happen. This is the bad option because it could cause the collapses of the individual market even before it takes effect.
2. They will repeal and replace. Most likely they will replace it with the new Health and Human Services Secretary's plan to keep the preexisting conditions protection plan, as long as you maintain coverage. If you don't maintain coverage you'll go into a high risk pool with higher rates until you maintain coverage for 18 months.
Plan 2 is very similar to what we currently have, but it replaces the punishment for not maintain coverage with higher premiums instead of a tax penalty.
What they should do is to increase the tax penalty to force more people into the pool and simultaneously add a public option, but that's not going to happen.