Windows – can’t boot into windows 10 bootcamp but partition is still good

Have you tried holding down the option key when you reboot? You can also select the default boot disk from the bootcamp GUI in windows.

To share with other users facing a similar situation, here is how I solved the problem--and avoided completely reinstalling OS X and Windows. For reference, my OS X version was Mountain Lion when I started solving the problem--and I needed to upgrade to Mavericks in the end.

1. Back up Windows partition with WinClone to an external HDD
2. Run "Backup now" in Time Machine to make sure I have a latest backup of OS X partition
3. Under OS X Disk Utility, remove Windows system partition (which is typically labeled BOOTCAMP)
4. In OS X Recovery boot, remove OS X partition and create it from the scratch (make it use whole HDD space)
5. Install a clean OS X (my MBA 2011 allowed only Lion--if I remember correctly, it's fine as long as it's not a later release than my Time Machine backup)
6. Restore my OS X partition from Time Machine. It makes Recovery Partition disappear, we'll fix it in the next step
7. From AppStore, reinstall Mountain Lion. It's only needed to re-create the Recovery Partition.
8. Under OS X Disk Utility, manually create a FAT partition for Bootcamp following WinClone support article. WinClone will convert it into NTFS in the next step.
   This is where you decide how HDD space will be split between OS X and Windows.
9. Restore Bootcamp partition from your backup (#1) to the Windows partition you created in #8.
10. Boot Windows under Bootcamp; it can run CHKDSK automatically, reporting that volume could be dirty--but didn't find any problems.
11. If you use Trackpad++, it needs to be reinstalled now. Boot Windows under Bootcamp, reinstall PowerPlan Assistant first, then Trackpad++.
12. Under OS X, re-create virtual machine in Parallels.
13. Upgrade to Mavericks.
14. Move to Bootcamp system partition all the data files that were originally stored on Windows data partition (provided you have their backup).

The only problem that's left at this point is that Parallels freezes VM when used in "all apps in one window" default mode (which is not Coherence, Fullscreen or Modality mode). Will seek solution for it later; at least it is stable for a week now in Coherence mode.

Before following the above sequence, I tried to recreate data partitition with Windows, converting the unallocated space that sized exactly like the lost partition. Failed: I found that there is a new partition which originally wasn't there: sized 620MB, but it didn't appear as recovery partition among Startup Disks on boot. Didn't try deleting it though, maybe it could help.