Skills with the (any) option works differently than multiplier "x2" options.
Skills with the (any) option all involve skill groups. These work differently than a single skill or talent like Sound Constitution. For starters, Dark Heresy specialties generally limit the skill groups you could purchase at a single rank. The rank would list the skill with a specific skill group, the player was not allowed to choose which skill group to take. For instance, a rank 3 priest (from Dark Heresy Core) can purchase both "Scholastic Lore (Imperial Creed)" and "Scholastic Lore (Legends)". He does not get to pick which skill group he takes for Scholastic lore.
When a player has the option to choose which skill group to take when purchasing a skill FFG lists it as:
"Exotic Weapon Training (Choose One)" - Example being a rank 2 Kroot from Into the Storm.
When a player has the option to choose which skill group to take for a skill but may purchase the advance multiple times in a single rank FFG lists it as:
"Exotic Weapon Training (Choose One) (x4)" - Example from the Xenographer advanced specialty from Into the Storm.
(This is how skill groups are listed with the muliplier option.)
There is no need to "choose one" with skills with the (any) option. The advance allows you to puchase any of the skill groups for that skill, the only limitation being the actual number of existing skill groups. This makes sense from a logical standpoint as well. Its not believable a character wouldn't be able to learn to pilot landspeeders and spacecraft, or a librarian could only learn one type of scholastic lore.
So yes, you may purchase skills with the (any) option multiple times. Paying the full cost for each skill group you purchase.