As far as it comes to Linux, the compiler/maker references libraries it can find through environment variables ($LD_LIBRARY_PATH, $PATH etc.) set globally or locally (in the script, possibly wrapping script or through the configure run) and in /usr/local/lib/, /usr/lib/ (...) most .so "files" are sysmbolic or hard links to the current versions of installed libraries beneath or in this directory.

For example /usr/share/lib/libld.so would be a link to /usr/share/lib/libld.so.5, so the compiler(s) are using the symlink to access the linked shared library file.

This means you don't have to delete library files, but change the links (look at the "ln" command) to point to the compatible library, if no direct reference was given in ./configure or passed to the maker/compiler through environment variables, the compiler will use the links to find the desired libraries. Normally you would not delete the newer libraries in /usr/lib in this case, but let the links point to the .so files having the right version number in their names.

Doing it in any other way would be quite a mess, it's done through links for ages in Unix and Linux, for good reasons.
Maybe Raspi Linux is an exception, i don't have a Raspi nearby at the moment to check, but i think basic things are done the same way here.

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