They will merge after some time....... and split up again when a new project is launched or when you upgrade to a new (major) BOINC version.
Actually, it may or may not split when you join a new project. If the new project assigns a CPID that is lower than the current CPID, it will not split for very long, as the new project will get the old CPID sent back to it. Since you are connecting to the new project, you can expect the split to be the length of your queue or less.
Upgrading to a new version will not in itself generate a new CPID, but if there is a major version change happening, and during the major verison change you join a new project that happens to generate a new CPID with a larger value than your current CPID, you will maintain the split longer.
The other way a split would be maintained for a long time is if a project were down for an extended period of time. e.g. S@H last month.
[EDIT] I just voted. None of the categories quite matches what I wanted to vote. I voted no. I do care about the split, but not enough to do much of anything because I expect them to be merged again sooner or later. Usually sooner.