The Benchmarq
BQ3287 is "Functionally compatible with the DS1287/DS1287A and MC146818A."
I'm not sure if that means that you can use it as a drop-in replacement. I'm a bit nervous about the term "functionally compatible."
The
DS12885, DS12887, and DS12C887 real-time clocks (RTCs) are designed to be direct replacements for the DS1285 and DS1287.
On the hard drive issue, it could be that the system BIOS does not support the newer hard drive (this was very common years ago), but it could also be that the system BIOS simply needs to be configured for the new hard drive. If the system has lost it's CMOS setup, the system might even need to be re-configured for it's
old hard drive.