I've come across some situations where I've made changes to a group of VIs or Objects and when it comes to close LabVIEW, LV conveniently forgets that certain things have changed. I say forget, but that's being nice because LV never seems to have known about the changes in the first place. If I rely on LV telling me what to save when closing a project, it often ends in tears. Re-loading the code can be broken as a result, or even worse, it might work but intriduce some hard-to-find bugs. Of course the solution would be to save rigorously, but I still think LV should try to keep things intact if possible.
- FIFO Reference settings on FPGA (Read, Write, Clear) settings are completely ignored. LV claims things have not changed, but they have.

- Changes to many LVOOP (.lvclass) properties. Again LV claims they have not changed, but they have.
Do others have more examples? Each time I get bitten by this behaviour I rage shortly but just get back to work. If we can try to get a list together, maybe it'll be enough to slap an idea on the Idea Exchange.
I'm using LV 2015,s o maybe things are better in the current versions?