I had the same problem and was referred to this thread. This was happening to me while setting up a template file in 2016. I will upgrade to 2017 soon but in the meantime I suspected the sections being purged out had something to do with the fact that I'd created 4 new section types and renamed Revit's Original "building Section" type. I've done some experiments. I've isolated the problem to be:
When you draw a section line using a specific type (e.g. Section Type 1) and then change the view type of the section (e.g. from Section Type 1 to Section Type 2) for some reason when purging the section is still "filed" under its original section Type (i.e. Section Type 1 in this example) so when you hit purge and Section Type 1 is selected - the section Type 2's also get purged...
I think for me a solution is to make sure that you have a section drawn of each view type that exists in the model - even if its a tiny one hidden somewhere. This will ensure that no Section Types get listed in Purge All window and therefore don't get purged out....
Unless of course you can upgrade your project to 2017, but if not at least this is a workaround