The most common and most likely answer to this crossword clue is the 7 letter word REHOMED
I've seen this crossword clue in Independent
R
E
H
O
M
E
D
Buddy explains!
The straight part
We know that "put in a new pen" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case put in a new pen = rehomed.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does REHOMED mean?
REHOMED verb- To find a new home for (especially a pet).
- To find a new family for (one or more adopted children) without using official adoption agencies.