Good for you for thinking outside the box with Piper and intervening for her! Sorry she has Lyme's but maybe once it is addressed and resolved you will see additional improvement. Our vet does a 30 days treatment of doxy. We dealt with Lyme's in Brodie last year. I too was shocked, don't hold your breath on them covering treatment but it's a bonus if they do. The vaccine helps, but does not prevent Lyme's. Ticks are active all year long, folks get comfortable in the winter but they are out there!
We used to do once a month hikes with a group I just love over in NYS pre Deacon days, but Brodie and I went once and as I gave him water after I noticed what I thought was a flea - hadn't seen one in YEARS and was floored! Sure enough, Brodie had picked up ticks and fleas on our hike - I am SOOOO allergic to flea bites. I used a lint roller and packed him up. As I am driving down the road I look down to see ticks on my jeans. I am SCEEVING at this point. I stop, lint roller me, Brodie, and drive as quick as possible to the nearest Walmart where I buy a flea comb, white towels and some topical. I doused my clothes, loaded Brodie into the back of my Yukon and on top of white towels, treated him in the back of their parking lot. I called my son warning him, stripped in our garage leaving my clothes in a garbage bag he left for me and ra upstairs in a towel, Brodie in my arms and washed us both in the bathtub. I have never returned to that park!
Do find out what Lyme's panel your vet uses. They used to do a series of tests which have been replaced with some new panels - sounds like what your vet is using but do read up and ask. Cornell has a Lyme's test panel and you also want full testing of ALL tick related diseases. Brodie started out 'depressed', then started a limp which, if I had not been on SN, I probably would have simply rested him until he got 'better' in my eyes. Minnie had recently been treated for Lyme's - first seen by Karen as a limp and I do believe there were others as well. Brodie tested negative first go round and we rested and all, but I was on high alert because of things I had read here. I did get Brodie assessed and treated by Ann's AWESOME chiropractor when we had a worse bout about a month later while we awaited results of another Lyme's work up but she too felt it was Lyme's. Be aware, Brodie ended up with both oxalate and once we cleared those up struvite crystals in his urine. I felt that him holding it for so long was the issue with these starting. I used Thomas Vets Cal Ox and to be honest, I don't remember if it was 1 bottle of 60 'treats' or 2 bottles, but I have 21 'treats' left. I gave him one nightly as a bedtime treat. My vets had never heard of them but were amazed - both crystals cleared up and our February pee re-check shows they remain gone. I use a plastic chicken treat feeder to collect urine. It's orange, about 24 - 30 inches long, has a 3-ish inch long tray that normally you'd stick out to give chickens treats so they don't nip you, but I sneak it in under the flow once it starts and collect urine. My local Agway has them currently at 1.00 - normally priced at 9.99 - ours was a gift.