Are the points coming back in ReCap - or just in other products like AutoCAD? If you see the issue in ReCap, this is likely because you also have the project loaded in another application like AutoCAD. This causes the optimization to fail. We've added a check for this in the latest hotfix (3.0.1.5).
If you only see the points in AutoCAD or Revit, you'll need to 'Save As' to remove the optimized points first. A bit of background:
There are now three 'levels' to how you can clean up a project:
1. The normal way - select points, delete them, repeat. This stores each operation just in the RCP file. When points are loaded from disk, each is compared against the operations and hidden if necessary. This can get slow as multiple overlapping selections are deleted.
2. 'Optmized' - upon saving, ReCap can optionally check each point against each operation and 'mark' it on disk. Once this is done, there is no need to keep the operations in the RCP like 1) above. ReCap can then very quicky show or hide each point instead of the costly checks.
3. Removing points on Save As - when you save a new copy of the project, ReCap can remove each deleted point. This effectively 'shrinks' each RCS file and the deleted points can never come back. As with 2), the operations can then be removed from the RCP.
Method 1 has been supported in AutoCAD/etc forever. Method 3 is supported by default since the points are simply gone. Method 2 however requires new engine support which will only make it into the other products in 2017. For compatibility with older products, you'll need to stick with 1) or 3) above.
Hope this helps,
Ryan
