In our backyard we have a kumquat tree which we purchased from non-observant Jews. When the tree was young, its fruits were tiny and orange – clearly kumquats. But now the tree has grown bigger and is producing large, round green fruits (looks like bitter orange). It seems, then, that the tree is kil’ayim. If so do we have to uproot it

The tree is clearly a hybrid with a bitter orange tree. However there is a safeik whether all citrus fruits are considered one species; if they are in fact one species, there is no prohibition of kil’ayim. Therefore, since there is a safeik whether the hybrid here is forbidden, one can be lenient and keep the tree. If one chooses to uproot the tree because he does not wish to maintain kil’ayim, he may do so and it’s not considered bal tashchis.