Since I updated to the latest version of kicad, I will open a project that we haven’t worked on in weeks due to having about 5 projects going at once. Some of the connections on the schematic will show they are connected but running the bug checker shows they aren’t connected, or the connections will just disappear all together. Any ideas how to keep this from happening? It doesn’t happen on projects I’m actively working on and opening daily, but I opened one today that hadn’t been opened in a couple months and it had no connects everywhere. I can obviously go back and fix the connections, but it takes man hours that we don’t have and we risk reconnecting something incorrectly if we don’t remember exactly how it was two months previous.
Do you mean the kicad nightly (will become kicad 5)?
If so then i fear it might be connected to the fact that the connection algorithm was actively developed until quite recently. So updating kicad could really have an influence here. (Especially if your schematic was made with a version using some older connection algorithm) This is one of the dangers of using nightly builds.
If you run kicad 4.0.x, then the update should not really have an influence.
In any case a screenshot might help us identify possible problems.
KiCad nightly has some new features to handle junctions, if that is what you mean? There may also be tweaks to connection cost. If you can post a sample file that would help a lot, otherwise we are guessing.