If Holdo is on a ship with only active charges, can she flip up a charge on a ship that does not have any active charges because the second ship does not have an active charge token?

I would say no, as Charges are not tokens. Going by the definition of "tokens" in the Rules Reference, tokens can be gained, removed and transferred and are either round (in Green or Orange) or diamond shaped (in Blue or Red). Charges can't be gained, removed and transferred and are not round or diamond shaped. I would probably classify Charges and Shields as their own thing as they have their own unique shape which are different from even a Marker, like Fuse markers or Condition markers, which are all hexagons or "tombstones" like the ID markers.

No, charges are distinct from tokens.

Standard Charges and Force Charges are listed under "Charges" in the rules reference (p. 7) and are always called charges (or use the symbol), not tokens. In contrast, Focus, Evade, Tractor, Ion, Disarm, Lock and Stress Tokens are all explicitly referred to as tokens.

Also, while the section on tokens in the Rules Reference does not provide a comprehensive list of tokens, it does describe how they behave (p. 19):

Quote

Some abilities cause ships to gain, spend, or remove tokens. Tokens are used
to track effects and come in a variety of colors.

• When a ship is instructed to gain a token, a token from the supply is
placed in the play area next to the ship.
• When a ship is instructed to spend a token or there is an instruction to
Remove a token from a ship, a token of that type is returned from that
ship to the supply.
• When a ship is instructed to transfer a token to another ship, it is
removed from that ship and assigned to the other ship.
◊ If a ship involved in a transfer is not able to remove or gain the token
involved, the transfer cannot take place.

When you spend a charge, you flip it from active to inactive rather than returning it to the supply. This is contrary to the rule for spending tokens, which would imply that charges are not tokens.