Your current work-permit broke the condition, now you have to make it complete again. I got many case was rejected when they renewed their work-permit because they entered Thailand with on arrival visa or tourist visa. The officer have checked it back on their passport.
Now you are holding work-permit, you have to enter Thailand with working visa only as non-b, non-o Thai spouse or Thai child, PR only. Date on booklet is valid but your last entry made it to be invalid.
I recommend you to apply new visa with current work-permit. After getting new non-b, you have to cancel your work-permit and apply new one. By the law, your work-permit is already expired because you entered country with tourist visa. Immigration officer and labour officer is very stick about this. You can't convert type of visa, extend visa and renew work-permit.
If you have high deposit on Thai Bank account or have letter of your pension, you can try to apply non-o-x at Thai embassy in your country. I have seen it from Thai embassy in Australia, England and USA
The immigration have a doctor to estimate date of stay base on the medical documents from the hospital, it’s not easy, if you are not admit in hospital, they will not provide 90days for you. Next time you can get the document again time extend.