Our crew disembarking from Panama are booked on the following flights:
PTY-CDG — Panama-Paris
CDG-HKG — Paris-Hong Kong
HKH-MNL — Hongkong-Manila
Does our crew need to have a visa/documentation from Panama since they will be having flight on Paris?
Filipino citzens need to get an airport transit visa in advance to transit in Paris. There are exemptions for people with valid visas from a few other countries (like the US or Canada) and for seamen (but possibly only when joining a ship in a French harbour) that might apply in some cases but generally speaking a visa is required.
As stated by Timatic, the database used by airlines:
Visa not required if traveling on duty and holding a Crew License or a Crew Member Certificate according to the Chicago Convention of 7 December 1944. Crew must wear uniform and duration of stay is according to the General Declaration.
For Hong Kong:
Visa not required for those arriving as Operational Crew for a stay of max. 7 days (extension possible).
So no, your crew does not need visas.