It seems there's one link in each device that's not the same, and restoring the device doesn't change that. For example, I have:
Device:
<isy.diag><title>Device Links Table : Office / 1A 17 13 1</title><insteon.lincs><eventInfo>
<ix>0</ix>
<ad>4088</ad>
<fl>162</fl>
<gr>0</gr>
<id>3905241</id>
<data>16719617</data>
</eventInfo>
<eventInfo>
<ix>1</ix>
<ad>4080</ad>
<fl>162</fl>
<gr>19</gr>
<id>3905241</id>
<data>16719617</data>
</eventInfo>
<eventInfo>
<ix>2</ix>
<ad>4072</ad>
<fl>0</fl>
<gr>0</gr>
<id>1834330</id>
<data>16719617</data>
</eventInfo>
</insteon.lincs></isy.diag>
ISY:
<isy.diag><title>ISY Links Table : Office / 1A 17 13 1</title><insteon.lincs><eventInfo>
<ix>0</ix>
<ad>4088</ad>
<fl>162</fl>
<gr>0</gr>
<id>3905241</id>
<data>16719617</data>
</eventInfo>
<eventInfo>
<ix>1</ix>
<ad>4080</ad>
<fl>162</fl>
<gr>19</gr>
<id>3905241</id>
<data>16719617</data>
</eventInfo>
<eventInfo>
<ix>2</ix>
<ad>4072</ad>
<fl>0</fl>
<gr>0</gr>
<id>0</id>
<data>0</data>
</eventInfo>
</insteon.lincs></isy.diag>