I've checked on one of the missing files. It was definitely OK when I used the pin_handler branch. A simple 1 version file. Never moved or anything.
Now it seems ssphys gets into trouble when parsing the database:

$ grep -Gre "ASJAAAAA" vss2svn.err
ERROR -- Attempt to add entry 'ASJAAAAA' with unknown version number (probably destroyed)

$ ssphys/ssphys info ~/OSrc/data/a/asjaaaaa | less
<?xml version="1.0" encoding="windows-1252" ?>
<File Name="/home/micke/OSrc/data/a/asjaaaaa">
    <ItemInfo offset="52">
... seems ok
    </ItemInfo>
    <CheckOut offset="416">
        <Comment><EC><D9>&#x12;</Comment>
        <ParentSpec><94>&#x01;</ParentSpec>
        <Computer><94>&#x01;</Computer>
        <Folder>^L<E5>&#x12;</Folder>
        <User></User>
    </CheckOut>
    <ParentFolder offset="1092">
... seems ok
    </Version>
</File>

The CheckOut entry seems to be full of garbage. Using the old version of ssphys, the entry comes out as:
    <CheckOut offset="416">
        <Comment>_</Comment>
        <ParentSpec>__</ParentSpec>
        <Computer>__</Computer>
        <Folder>__</Folder>
        <User></User>
    </CheckOut>
    <ParentFolder offset="1092">
Which seems better, but not entirely good.
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