My secondary hard drive disappeared in windows and when I restart the DOS booting takes like 15 mins while it shows the "Starting Windows" logo.
How to solve this problem? Also how can I retrieve the files from this HDD?
If your drive is a Western Digital one, it is a bug in the Module 32 of the HDD firmware. Those thing may happen:
The linked post says that the fix can be done by a normal user, but it is risky. If the data stored in the drive is important, you can send it to a data recovery company, and with the right tool they can do it with 3 clicks, so don't let them charge you exorbitant prices.
And do not try to use a refurbished drive, it is sure to fail again.