Formatting Hard Drive for secondary drive without losing recovery partition

You can do it safely. The important point to recognize is that Formatting and Partitioning are two different tasks. Recent versions of Windows make it easy to do these on a new empty drive by combining them into one Wizard, but the separate steps are still maintained. Only the automated process is made easier.

In earlier versions of Windows, on a new empty disk you FIRST had to Create a Partition. That reserved a chunk of space to be used as a drive. You have the option of using all of the HDD's space in this one Partition, or of making it smaller than that. The Creation of the first MBR Partition also creates the disk's Partition Table in a particular fixed location on the surface, which contains the details of all its Partitions and which is limited to no more that 4 Partitions because that's all the space allowed in the MBR Partition Table structure. Once that has been done, you can Create more Partitions (up to 4 total) from the remaining Unallocated Space. Doing that in each case simply enters the appropriate data into that Partition Table. Now any system accessing the HDD can read the Partition Table (it's at a known "standard" location) and find out exactly where each Partition is and use them.

AFTER one or more Partitions are created, each must separately be Formatted. Formatting writes the necessary files to that ONE Partition to create the File System on it. A Format operation is carried out on only ONE partition at a time, and does NOT affect any other Partition. Only after BOTH operations have been completed can your OS access a Partition and use it for data.

So in your case, OP, you most certainly CAN do a Format only on one Partition without affecting any other. Just be VERY careful that you do that on the Partition you want to wipe clean, and not on one you want to save. I would suggest you do a Full Format, which can take hours. This process will test every Sector in that Partition and write useless zeroes to them. In the process, if it finds any that are not working properly, it will make them as Bad Sectors in Windows' files on that "drive" and prevent Windows from ever trying to use them. (A "drive", by the way, is one Partition that Windows gives a letter name to and treats as one storage unit called a "drive". To Windows, the term "drive" does not necessarily mean an entire HDD unit's space.)