Hi Chris!
Since I started this “Ally Bank not syncing” thread, Tiller has released an automatic update which I’ve applied to my spreadsheet. Since that update may have made substantial changes behind the scenes, I’m wary of trying to offer a definitive answer to your question, so instead I’ll offer a few thoughts regarding each level of safety mentioned above.
What Do We Mean By “Safe”?
There are different levels of “safe”:
- Fiscal safety / Bank Data safety — Tiller is inherently safe inasmuch as they can modify neither your bank balance nor your bank’s data.
- User-entered Data safety — Google sheets is mostly safe inasmuch as it saves versions of your document as changes are made. (see below)
- Time safety — Here’s where nothing’s safe…addressing problems with your spreadsheets will take time, one way or another. I suspect your question boils down to, Can you save me some time?
I doubt I can save you a ton of time, but hopefully something below will at least save you some. 
So. Let’s drill down on the 3 levels of safety.
Fiscal safety / Bank Data safety
At this level of “safe,” the answer to your question is, “Yes!” You can always link to a completely new spreadsheet and have a pristine setup with 100% clean data from your bank.
User-entered Data safety
Any time you edit your sheets by hand, there’s always the risk that you’ll make a mistake that a computer would not have made. In this sense, the answer to your question is, “Not entirely,” however, there’s something you can do to at least get much closer to safe: use version control.
I like to tinker with things. It helps me learn, which gives me a greater sense of control. That’s part of what I like about Tiller. I’ve also broken my spreadsheet in the past by not following this simple best practice: save a named version before making any major changes. How?
File > Version history > Name current version.
This way, if you do something horribly wrong, you can always find where you started in the version history for the spreadsheet. It’s not a panacea as any transactions Tiller adds after your named version could be “lost” if you end up having to revert. Such a situation could have you futzing with copy/pasting rows to effectuate a “merge” from multiple versions, which, depending on your point of view, is either more learning…or a big waste of time. 
Still, it’s well worth your while to learn about Google Sheets’ version system, one way or another. If you aren’t already familiar with it, I highly recommend creating a blank spreadsheet and just messing around to get a feel for how the version history and named versions work.
Time safety
If the prospect of having to delve into the bowels of your spreadsheets doesn’t appeal, it might be best to avoid deleting anything. In fact, if I were in the same boat now as I was a month ago, I’d probably handle your situation (such as I understand it from your single sentence 
) this way:
- Create a new spreadsheet and link it to Tiller, as if starting from scratch.
- Copy/paste any transactions from my old spreadsheet that aren’t present in the new one. (I’m not entirely sure how many months of history Tiller preserves on their-, or Yodlee’s, servers.)
- Copy/paste whatever customizations I’ve made to my categories, autocat, etc.
This approach has the benefit of being entirely disposable…if you make a mistake, the new spreadsheet can be deleted with no harm to the original.
Good luck!
– Other Chris