Sync of products and orders between Zoho Inventory, Zoho Books and Shopify

Sync of products and orders between Zoho Inventory, Zoho Books and Shopify

Good Day

I migrated from QuickBooks to Zoho Books and Zoho Inventory at the beginning of this year. The migration team assisted with importing my data, but I am currently experiencing multiple issues affecting syncing between Shopify and Zoho.

1. SKU & Product Name Mismatch

  1. QuickBooks assigned SKUs to products during migration.
  2. These SKUs did not match the SKUs in Shopify.
  3. I had to manually assign SKUs in Shopify, which became time-consuming.
  4. As a result, many product names and SKUs in Zoho now reflect the QuickBooks versions rather than Shopify.
  5. Because of this mismatch, Shopify and Zoho Inventory do not sync correctly.
    1. I now have:
      1. Many inactive products
      2. Duplicate or mismatched items
      3. Products linked to historical invoices that cannot be deleted

Question:
What is the most efficient way to realign Zoho Inventory SKUs and product names with Shopify without affecting historical invoices?

2. Inventory Going Negative

When a Shopify order syncs:

  1. It creates a Sales Order in Zoho
  2. Zoho adjusts stock
  3. Stock levels go into negative quantities because inventory quantities were never properly aligned during migration

Question:
What is the correct way to reset and realign inventory quantities between Shopify and Zoho without breaking historical data?

Would it help to:

  1. Temporarily disable syncing?
  2. Perform a full stock update via CSV?
  3. Re-map items completely?

3. Multiple Locations Issue

During migration:

  1. A "Head Office" location was created
  2. I already had a "My Company Name" location
  3. Stock is now split between the two locations

Stock does not automatically move between locations and I must manually transfer it.

Questions:

  1. Is there a way to bulk transfer stock between locations?
  2. Can one location be merged or deactivated safely?
  3. Which stock value (physical vs accounting) is used when invoices are created?

4. Shopify Orders → Invoice Automation

Currently:

  1. Shopify orders sync as Sales Orders
  2. I must manually convert them to Invoices
  3. I do not want invoice numbers to share the same transaction series as manually created Zoho invoices

Questions:

  1. Can Shopify-generated invoices use a separate transaction series?
  2. Can invoices be created automatically and marked as Paid?
  3. How can I prevent the system from emailing customers payment reminders when they have already paid via online gateway (weekly payout model)?

5. Operational Concern

I am currently managing this system alone and the manual corrections required are very time-consuming. I would appreciate guidance on the most efficient way to:

  1. Standardize SKUs
  2. Correct inventory quantities
  3. Consolidate locations
  4. Automate Shopify → Invoice → Payment flow correctly

Kind Regards,
Nelmarie