[RPG] Channeling Ally Spirits

Essence can be recovered, but it's very difficult. By default, removing cyberware leaves an Essence "hole", into which new cyberware can be installed. In 3rd Edition, Man & Machine handled several different ways for Essence costs to be modified via surgery and the like, and things like delta grade cyberware can decrease Essence costs, as can certain qualities, but it's not possible to regain Essence by itself.

Until 4th Edition's Augmentation came out, at least. It's technically not SR5, but it's part of 4e which is pretty similar, and better yet it's some of the parts that don't have mechanical changes between editions.

Revitalization is a recent breakthrough that repairs Essence loss derived from invasive implantation. Universal Omnitech is trying to keep the mechanism a secret, though geneticists have speculated that the effect is achieved by performing somekind of “genetic feng shui.” (Augmentation, p. 88)

So, in short, yes, it is possible to restore Essence loss after removing the implant, but it's difficult and expensive, not to mention time consuming (.1 Essence a month, and 20k per month, plus a hefty start-up fee). That said, it might be more readily available in 5th Edition.

In addition, I wouldn't be entirely unsurprised to see a metamagic for this at some point, especially since it's the sort of thing that I associate with Shadowrun's metaphysics (more from Adepts on the Earthdawn side) advancing to a certain point.

Basically: Not really, unless they're pretty sloppy and don't counter your Astral Tracking. Although spirits might not be as unstoppably dangerous as you think.

Any spirit influencing material matters will leave a material trace, just like any physical being - because they must materialize to affect the material world.

If a spirit wants to affect anything on the physical plane, it has to materialize first (p. 314). It gets physical attributes based on its type (Spirits, p. 303) and appears as a solid, physical version of its astral form—it’s relatively solid even if it doesn’t look solid, like a spirit whirlwind or a water elemental.

The spirit is going to leave some kind of physical trace at the scene, and an astral impression wherever it travels. That will fade relatively quickly though, and the mage can wipe it clean - so you're right, it is quite a challenge to track a summoner who wants to stay hidden when you arrive on the scene way too late. Just as it would be hard to track down a Rigger who used a sniper drone, or to find a decker who stole your files, or to find a sneaky assassin, 8 hours after the event when they've covered their tracks.

You do, however have Astral Tracking to fall back on if the mage hasn't erased their tracks everywhere the spirit has been.

Furthermore it seems to me that the astral signature vanishes with the spirit.

I'm not seeing where that's the case in the rules. You've even got a "+1 for every hour since the link was active" mod in the tracking threshold table (p315), which indicates you can track stuff that happened in the past after the link is gone as well as things that are happening now. If a spirit was there 4 hours ago, for example, this would suggest you can trace its origin at a +4 threshold (and tracking master by spirit is a +0 modifier for bound spirits, or +2 if it wasn't bound).

On the theme of danger...

A nonawakened person is pretty much helpless against a spirit

This isn't necessarily the case.

The materialization thing means that even unawakened victims can defend themselves quite effectively. Once the spirit materializes to make its assault they can physically attack it just like any metahuman opponent. Spirits do have all manner of freaky powers, and can more easily sneak up on the unawakened, but they still go down if you pump them full of bullets. Even before they materialize you've got a chance of spotting them:

Physical beings may sense when an astral form passes through their aura. Make a Perception + Intuition (4) [Mental] Test—you receive a +2 dice pool bonus if you’re Awakened. If the test is successful, the character feels slightly breathless, and they experience a chill or tingling sensation from the passing of the astral form. Security personnel are trained to recognize this feeling as a sign of an astral intruder.

Dangerous, yes, but not really any more so than other sneaky backstabbers who might try to kill you.