Question:
What should you do if you need the bathroom after Shmonei Esra with your tefillin during Shachris? When you take them off, do you have to cover them with your tefillin bag, and when you come back, do you have to put them back on?
Answer:
Hello,
You should put them back on for asrei and uva l’Tzion, although there is controversy if a bracha should be said on them when putting them back on. There are different customs regarding this. The Sefardi custom is to say a bracha, and the Ashkenazi custom is controversial, and many don’t say a bracha on them, especially if a urinal was used, and not a real bathroom.
Regarding covering the tefillin, I have seen people doing this, but I don’t know the reason or sources for it.
Sources:
ע' ס' כ"ה סע' י"ב ומ"ב ס"ק מ"ז, ביה"ל ד"ה ו"יא וד"ה והכי נוהג, וע' ג"כ בפסקי תשובות ס' כ"ה אות כ"ג למ"מ בזה.