I run DPA for our SQL Servers and am configuring a new server that I may want to run DPA on while setting up, but would have to borrow a license from another server. If I deactivate a server license and then re-activate it later would the history be preserved, and simply have a gap in the data while it was inactive?
You are exactly right. Basically the idea is that any data collected while validly licensed is your data (we don't do anything to it except summarize per normal).
You can move licenses around as needed.
Now, keep in mind that excessive movement of licenses could cause repository bloat as we'll keep 30 days of detail for each instance being monitored or having BEEN monitored.