I don't believe its your configuration that is somehow flawed. I can not speak to total certainty on it, but i think you have realized two limitations.
For the "." (period) this is most likely reserved since LDMS queries themselves use them to separate the folder levels within the inventory itself. As for the "-" (hyphen) that might be an SQL type of reservation. I'm not sure of this, but you have to keep that in mind as well. There is only so much that LDMS queries can do, since in the end they do have to translate to SQL queries, and there are specific things that can't be done in SQL due to its code logic.
You can't add those items directly to the LDAPPL3.template file anymore you have to use Manage Software List > Custom Data > Registry Items.
Not true... Still documented in Help
and it would be (IMHO) a poor choice to remove the ability to bulk import info even if its limited by memory.
I found the amount of reg keys I could import changed with more or less memory or so it seemed...
Editing the file is still supported but not for registry keys, that has been taken into the GUI. That is why things are getting overwritten, because the DB is where this stuff is stored now.
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So let my pain help. As usually there is a lot of confusion here due to poor documentation. Registry keys are supported when using the ldapp import method. I keep a txt file of all my ldapp modifications since as you discovered, they are removed after importation.
The issue here is there is a nasty bug in the importation process. It pretty much chews up the syntax, adds weird periods, changes the case, etc... This is fixed in SP1 and the fix will work with base 9.5. I'm in sick in SLC and don't feel like pulling up my core (no energy). Just open a case and ask for Zman isue with ldapp imports and support will take care of you. THe weird case changing is not fixed, but I can live with that for now.
Problem / Suggestion ID : 70036