Most likely, yes, you'll need to recompile them. There's a remote chance it might not be required — this would be under the following circumstances:

• the FreeTDS libs are 100% interface (API) and binary (ABI) compatible with the Sybase libs, i.e. a drop-in replacement (not sure if this is the case)
• the new libs are actually found at runtime (e.g. via appropriate LD_LIBRARY_PATH settings)

You can always check with ldd which dependent libraries are being pulled in (if any) by your old DBlib.so and CTlib.so. Make sure you call it from within the right environment.